How to Set Up an Electronic Filing System for your Scanned Documents

Electronic filing system - windows

Many businesses are abandoning paper-based record keeping methods in favor of the convenience and security provided by electronic document management.

After all, a paperless world is simple, efficient, and environmentally friendly. 

However, transitioning from a paper to a digital filing system isn’t as straightforward as it may seem. There are many pitfalls that can be encountered along the way, demanding thoughtful preparation well before the first document hits the scanner. 

As more of the information we store is stored digitally, organizing it effectively becomes increasingly difficult. This is especially true for businesses who need to manage a large number of records.

Ensuring these records are accessible is crucial for your business, not only operationally, but for compliance reasons, presenting significant challenges both during and after the scanning process. 

In this guide, we’ll explore some of the considerations you’ll need to make when organizing your scanned documents digitally.  We’ll also provide a step by step roadmap you can follow to set up an electronic filing system that will help your business manage your digital documents effectively and securely.

First up: What is an electronic filing system?

An electronic filing system (often abbreviated as EFS) is a method of organizing and managing digital documents in a structured manner for easy retrieval, access, editing, and management. 

Unlike traditional paper-based filing systems, an electronic filing system stores documents in a digital format (typically PDF or TIFF) on servers, in cloud storage, or within specialized EMR software.

These systems typically include features for indexing, searching, and categorizing documents, which makes it easier to locate and retrieve the information you need. 

Security features like encryption and user access controls are often implemented to protect sensitive information as well.

The benefits of an electronic filing system include:

  1. Efficiency: Digital files can be retrieved and shared much more quickly compared to searching through file cabinets or bankers boxes for paper documents.
  2. Space-Saving: Digitizing files significantly reduces the need for physical storage space, thus eliminating the necessity for expansive file rooms or external storage facilities in an office setting.
  3. Security: With proper encryption and access control, digital files are more secure than paper files, which can be misplaced, stolen, or damaged very easily.
  4. Accessibility: Digital files can be stored in the cloud and accessed remotely, allowing for a flexible work environment.. 
  5. Sustainability: A paperless system is environmentally friendly, cutting down on paper waste and the energy costs associated with maintaining physical storage.
  6. Collaboration: Physical documents can only be in one person’s hands at any given time. Electronic systems often allow multiple users to view or edit a document simultaneously.
  7. Cost-Efficiency: Over the long term, electronic systems are more cost-effective, reducing office expenses like paper, ink, and physical storage space.
  8. Compliance: Many systems offer features that help businesses comply with data privacy laws and regulations such as automated document retention and disposal.

For businesses, adopting an electronic filing system can be a significant step towards modernization, cost reduction, and sustainable practices.

Things to Consider Before Setting Up an Electronic Filing System

Creating an electronic filing system requires thoughtful planning to ensure that the system meets your needs, integrates smoothly with your existing workflows, and complies with regulatory standards. 

Before diving into the specifics of software, storage, and organization, let’s explore some key considerations that can guide you in setting up a paperless filing system that’s efficient, secure, and sustainable.

Understanding Your Document Categories

Most businesses, regardless of their size or industry, grapple with an array of documents that must be retained for various operational, legal, or historical reasons. Understanding these high level categories can help you build a file hierarchy that is logical and intuitive. 

It’s also common for these document categories to be relevant to different departments within your organization. 

For example, the finance team may frequently access invoices, while the HR department needs quick access to employee records. Given this, organizing your documents by category becomes an intuitive and practical approach to ensure that each team can easily find what they need when they need it.

To visualize this, consider a basic file structure that could serve the needs of an average business:

  • Finance
    • Invoices
    • Tax Records
    • Expense Reports
  • Human Resources
    • Employee Records
    • Benefits Information
    • Compliance Training
  • Sales and Marketing
    • Client Contracts
    • Marketing Campaigns
    • Sales Reports

With a categorized structure like this, you’re setting the stage for a more organized, efficient, and manageable digital filing system.

Understanding Indexes

Streamlining access to important documents isn’t just a convenience—it’s a game-changer for your business. 

When your employees can locate the information they need quickly and efficiently, everyone benefits: customers receive better service, vendors experience more efficient transactions, and employees themselves can focus on job specific tasks rather than sifting through piles of paperwork.

Proper indexing during the scanning process is the secret sauce that makes all of this possible. Meticulously tagging your digital files with key identifiers extracted from the original documents like invoice numbers, names, or any other unique identifiers enables text-based searches that can help employees locate information near instantaneously.

Carefully selecting your indexes from the outset will ensure you’re able to build a strong organizational foundation you can build upon for years to come. 

Navigating the intricacies of file indexing can be a challenge when you’re handling your scanning project in-house. 

At SecureScan, we simplify this process by providing a primary index for your documents free of charge. We will extract the relevant identifiers and embed your documents metadata that can be quickly searched, helping you get the most out of your digital files.  We even offer the flexibility to add indexes for an additional fee. 

Address Security Concerns

Ignoring security while setting up your digital filing system is like leaving your front door wide open while you’re away; it invites a myriad of problems ranging from data theft to unauthorized access and even compliance violations. 

Unsecured files can be manipulated, copied, or deleted, putting the security of your data at risk and increasing the potential for legal repercussions against your business.

Thankfully, storing your records digitally provides your business with a whole host of security features you can use to protect the security of your information including: 

  1. Role-Based Permissions: Limiting access based on job role is an excellent way to reduce the risk of unauthorized handling of sensitive documents. For instance, while your HR team may need access to personnel files, they shouldn’t be browsing through financial reports, and vice versa. 
  2. Encryption: Encrypting your files adds a robust layer of security, making the data unreadable to anyone without the appropriate key or password. This is especially crucial for protecting confidential and sensitive information.
  3. Two-Factor Authentication (2FA): Implementing 2FA means that even if someone gains access to a password, they’ll need a second form of identification to access your files.
  4. Regular Backups: While not directly a security measure, regularly backing up your files ensures that you can quickly recover data in case of accidental deletion or a cyber attack.
  5. Firewall and Antivirus Software: These serve as your first line of defense against external threats and should be a staple in any digital security setup.

Properly securing your electronic filing system brings about several benefits:

  1. Compliance: Many industries have strict guidelines regarding data protection. A secure filing system helps ensure that you’re in compliance with these laws, mitigating the risk of legal complications.
  2. Trust: Knowing that their sensitive information is secure makes both employees and external stakeholders more comfortable and trustful of your organization.
  3. Operational Efficiency: A secure system is a reliable system. Reduced risk of data loss or theft means operations can proceed smoothly without the disruptions that security incidents can cause.

So, as you set up your digital filing system, remember that security isn’t just an optional add-on; it’s a critical component that protects your business on multiple fronts.

Plan Ahead for Flexibility

As your business evolves and market dynamics shift, you’ll need a filing system that can adapt without causing operational hiccups. A flexible digital filing system isn’t just convenient; it’s future-proof. The last thing you want is to find yourself tethered to a proprietary system that locks you into one ecosystem, constraining your options and potentially hampering your business’s growth and adaptability.

So what elements contribute to a flexible electronic filing system?

  1. Scalability: Choose a system that can grow with your business. You should be able to add more storage, users, or features without having to overhaul the entire setup.
  2. Interoperability: Opt for a system that plays well with others. Your digital filing system should be able to interact seamlessly with different platforms, be it your CRM software, accounting tools, or any other systems you use. This ensures that you’re not stuck in one particular tech ecosystem.
  3. User-Friendly Customization: A flexible system allows for easy customization without requiring specialized IT skills. This could range from creating new folders and tags to defining unique user permissions.
  4. Cloud-Based Options: Cloud storage solutions usually offer more flexibility than local servers, as they allow for easy access from different locations and devices. However, do consider security implications and choose a reputable cloud service.
  5. Open Formats: Save your documents in formats that can be easily accessed by different software. This will prevent you from being tied down to specific programs for viewing or editing.
  6. Easy Migration: Whether you’re moving to a different platform or upgrading your current one, data migration should be straightforward. Look for systems that offer easy export and import options.

By prioritizing flexibility when setting up your digital filing system, you position your business for both immediate efficiency and long-term adaptability. You’ll be able to pivot more easily as market conditions change, and your filing system will be a robust tool that helps—rather than hinders—your growth.

Think About Future Compatibility Issues

Your digital documents might need to be accessed from various devices or shared with others. Ensure that the system you choose is compatible with multiple platforms.

If your team works on a variety of devices, like laptops, tablets, and smartphones, you’ll want to make sure that your digital filing system is compatible across the board. 

Compatibility isn’t just a tech spec; it’s a catalyst for streamlined collaboration and productivity. When your file system is compatible with multiple devices and operating systems, sharing files among team members becomes a hassle-free process. No one needs to waste time converting files or grappling with access issues; instead, files can be opened and edited right away, whether someone is in the office on a desktop or in the field using a mobile device.

But compatibility doesn’t end with everyday operations. You should also consider the long-term portability of your digital filing system. Why? Because business needs change, technologies evolve, and there may come a day when you’ll want—or need—to migrate to a different system. If the filing system you set up initially is built around widely-accepted standards and formats, you’ll have the freedom to make that switch without running into major roadblocks like data loss or cumbersome file conversions.

So, as you’re setting up your digital filing system, give due thought to compatibility. Make sure it aligns well with the devices your team uses and that it’s portable enough to adapt to future technological shifts. This foresight ensures that your system serves you well today and remains a flexible asset for your business in the years to come.

Assess Your Legal Requirements

When it comes to your legal requirements, it’s crucial to note that each industry has its own set of regulatory standards that must be adhered to, in addition to state mandated record retention schedules and federal privacy protection laws

These regulations often dictate how long records must be kept, who can access them, and how they should be safeguarded. 

Failure to maintain compliance doesn’t just put your data at risk—it can result in hefty fines, legal repercussions, and damage to your business reputation. So, it’s not just about keeping things tidy; it’s about playing by the rules that keep both you and your customers secure.

Evaluate Your Accessibility Needs

When it comes to evaluating your accessibility needs, it is important to consider who in your organization needs access to your files. 

Ensuring that the file system or storage solution you choose aligns with these access requirements is crucial for your operations. 

The easier it is for team members to find and collaborate on documents, the more efficiently your business is likely to run. 

So, when mapping out your digital filing strategy, remember that improved accessibility doesn’t just make individual tasks easier; it can also be a game-changer in fostering teamwork and collaboration.

How to Set Up an Electronic Filing System

Setting up an electronic filing system is not just about transferring your physical files into a digital format; it’s about organizing those files in a way that makes them easily retrievable, secure, and future-proof. Let’s walk through the key steps involved in setting up an efficient electronic filing system.

1. Create a Document Retention Plan

Before you digitize a single document, create a plan that outlines which documents need to be kept and for how long. Whether it’s tax records, client contracts, or employee files, different documents have different retention requirements. 

Software solutions like an electronic records management system can automate the retention schedules for you, but it’s good to know the basics yourself. A well-crafted document retention plan ensures that you’re neither hoarding unnecessary files nor deleting important ones.

You can read our guide on creating a document retention plan here.

2. Choose a Storage Solution

There are a number of different ways to store your digital files, and choosing the right one for your business depends on your specific needs.

  • Self-hosted SFTP: An SFTP is a secure file transfer protocol that uses encryption to send and receive file transfers securely. It offers the highest level of control, but requires you to maintain your own servers. It’s especially useful for businesses that need to manage large amounts of sensitive data.
  • Dropbox: Dropbox provides cloud storage solutions that can be accessed from virtually anywhere with relatively little setup required. It offers a user-friendly interface and is an excellent choice for small to medium-sized businesses. However, you’ll need to trust a third party with your data which may not meet your security standards.
  • Document Management System (DMS): A DMS is software that not only stores documents but also offers features like version control, metadata tagging, and advanced search capabilities. This is a comprehensive solution designed for businesses that require more than just storage, enabling you to manage the entire lifecycle of a document.
  • Operating System Organization: For smaller operations or individual use, simply using your computer’s file system (like Windows File Explorer or macOS Finder) might suffice. Utilizing folders within your computer’s native operating system or a local shared drive is simple and cost-effective, but not ideal for larger businesses with more complex needs.

Regardless of the option you choose, always have a backup, preferably in a different location, to secure your data.

3. Secure Your Files

When transitioning to an electronic filing system, it’s crucial to understand that your files are only as secure as the system you place them in. Several types of security measures are commonly employed to ensure the integrity and confidentiality of your digital files.

  • Data Encryption: This involves converting your files into a format that can only be read with the right encryption key. Modern encryption algorithms like AES (Advanced Encryption Standard) provide robust security.
  • Two-Factor Authentication (2FA): This adds an extra layer of security by requiring two forms of verification before allowing access to your files—often a password and a temporary code sent to your mobile device.
  • Firewalls: These act as barriers between your file system and unauthorized access from the internet. They monitor incoming and outgoing network traffic based on an organization’s previously established security policies.
  • Regular Software Updates: Many vulnerabilities come from outdated software. Consistently updating your storage solutions to the latest version will help you benefit from ongoing security patches.
  • User Permission Levels: Define who can do what within your filing system. For instance, some users may only have permission to read files, while others might have the ability to edit or even delete them.
  • Activity Monitoring: Many advanced systems offer the option to track who has accessed, edited, or deleted files. This is crucial for internal audits and can be vital in identifying the source of a security breach.
  • Virtual Private Networks (VPNs): A VPN provides a secure tunnel for your internet connection, making it much harder for anyone trying to intercept your data transfers.
  • Secure Socket Layer (SSL) and Transport Layer Security (TLS): These technologies encrypt the data packets that are sent between the user’s browser and the server, ensuring the data transfer is secure.

By understanding and implementing a mix of these security measures, you can create a robust electronic filing system that not only stores your data but also protects it from various vulnerabilities. The choice of security measures may depend on the nature of your business, the types of documents you’re storing, and compliance requirements you may be subject to.

4. Maintain the System

Your filing system isn’t a “set it and forget it” endeavor. Regular audits can identify bottlenecks, uncover security vulnerabilities, and reveal opportunities for improvement. Consider archiving older files that are no longer needed but still need to be retained for legal reasons, to keep your system lean and easy to navigate.

5. Train Your Employees

Implementing a new system means nothing if your team doesn’t know how to use it effectively. Training programs and refresher courses can help employees get accustomed to the new setup. 

Keep in mind that everyone won’t be on the same tech-savvy level, so offer multiple training methods to suit different learning styles. Be prepared for some resistance and difficulties during the transition period, but stay committed to resolving them to ensure a smooth operation in the long run.

You can try a mix and match of the following to help get your employees up to speed:

  • Workshops & Training Sessions: Ensure that your team knows how to use the system effectively.
  • Continuous Feedback: Open a channel where they can report issues or suggest improvements.
  • Anticipate Challenges: Know that there might be hiccups along the way, from tech issues to user errors. Be patient and persistent.


By following these steps, you’ll be well on your way to setting up an electronic filing system that meets your business needs while also being secure, efficient, and flexible for the future.


Setting up a paperless office by creating an efficient, secure, and flexible electronic filing system is not just a trend; it’s a necessity for modern businesses. It allows you to quickly retrieve files, safeguard sensitive information, and easily adapt to future business needs. 

If you’re looking for professional assistance to make this transition seamless, SecureScan is your go-to solution. We offer secure document scanning services that make it easy for businesses to transition away from paper. With over 21 years of experience, advanced security measures, and metadata tagging, SecureScan ensures your move to a paperless environment is as smooth as possible.

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