How to Prepare for eCTD Submissions Without Buying the Software Yet

If your biotech or pharma start-up is preparing to submit its first IND to the FDA, you've probably heard about the electronic Common Technical Document (eCTD) format.

And maybe your first instinct is: “Time to buy eCTD software.”

Not so fast.

Yes, eCTD submission software is essential—but not necessarily right now. For many early-stage companies, especially those still drafting modules or gathering data, there’s plenty you can do to prepare without spending thousands on a system you’re not ready to use.

In fact, prepping early and strategically will save you time, reduce vendor stress, and help ensure a smooth submission when the time comes.

Here’s a roadmap for how to get organized now—before you commit to tools.

1. Know What You’ll Be Submitting in your eCTD Submission

Start by understanding the structure of the eCTD. Even without software, you can organize your documents to align with the FDA's required format:

●        Module 1: Region-specific info (e.g., forms, cover letters)

●        Module 2: Summaries

●        Module 3: Quality (CMC)

●        Module 4: Nonclinical study reports

●        Module 5: Clinical study reports

✅ Smart IT Move:

Use a structured folder system that mirrors the eCTD format. This not only helps your team stay organized—it reduces the effort required by your publisher later.

2. Use Clear, Consistent File Naming Conventions

The FDA expects document filenames to be short, unique, and descriptive. But this is about more than just compliance—it’s about making life easier for everyone reviewing your IND, internally and externally.

✅ Smart IT Move:

Adopt submission-friendly naming conventions early. No need to get fancy: stick to all lowercase, short but descriptive filenames with no special characters except hyphens. For example, 32s13-gen-prop.pdf is far superior to CMCprocessFINAL_updated2.pdf. (Ideally your document management solution plus a comprehensive tracker are taking care of version control, but in a pinch, you can append the date and last author initials to the filename during the authoring phase, e.g., 32s13-gen-prop_30may2025-sed.pdf.)

3. Track Document Status and Ownership

One of the biggest pain points in preparing for submission is figuring out which documents are done, which are in process, which are still pending, and who owns what.

✅ Smart IT Move:

Use a submission tracker spreadsheet with:

●        Module and section

●        Document title and filename

●        Author / responsible party

●        Authoring status (Draft, In Review, Final)

●        Formatting and/or Submission Readiness status

●        Publishing status

You can also track supporting information like references, hyperlinks, and cross-references—long before you need to validate them.

4. Write With eCTD in Mind

Even if you’re still writing study reports or summaries, writing with submission in mind now prevents rework later.

✅ Smart IT Move:

Ask your team to follow these FDA-friendly writing practices:

●        Use standard section headers

●        Eliminate embedded attachments or hyperlinks that won’t resolve in the submission package

●        Use bookmarks and internal links where appropriate (and ensure they’re working!)

●        Make sure you indicate where external hyperlinks will be needed, typically by turning the font blue. And remember, external hyperlinks can only be created to documents or sections within documents – not to eCTD headings that contain multiple documents (e.g., publishing can create a hyperlink to 3.2.P.3.1 but not to 3.2.P).

5. Get Your Documents Ready to Be Submission-Ready

The FDA has specific formatting requirements for PDFs, but meeting those requirements starts during authoring. Preparing compliant documents as you go with software you probably already have (Microsoft Word and Adobe Acrobat) can save you a lot of time and headaches when the time comes for publishing.

✅ Smart IT Move:

Ensure your documents:

●        Are text-based (not scanned) PDFs (and if you do have to use scanned documents, make sure they undergo Optical Character Recognition [OCR] with a quality tool like Adobe Acrobat).

●        Include Tables of Content for documents with 5 or more pages

●        Have no security settings (no passwords or locked permissions)

●        Use consistent fonts, margins, and headers

●        Use captioning and cross-referencing tools to create internal hyperlinks

This work can be done in parallel with writing and QC—long before publishing software comes into play.

6. Choose the Right eCTD Vendor—But Don’t Buy Yet

Eventually, you’ll need a tool or vendor to compile, validate, and submit your application. But waiting to license eCTD software until your documents are nearly final can save you money and reduce learning-curve stress.

✅ Smart IT Move:

Interview vendors early, understand your pricing options, and budget for submission support – but don’t rush the software purchase. Some vendors even offer à la carte publishing services or “pay per submission” models that may suit your stage better than an annual license.[2] [3]  Ensure you have the right knowledge and talent on your team (either as contractors, full-time employees, or dedicated, right-size vendors) to support your software and submissions.

Final Thoughts: Strategy Before Software

Buying eCTD software is important—but it’s not the first step. Smart companies start with strategy: document structure, naming, formatting, and status tracking.

By laying this groundwork now, you’ll:

●        Accelerate submission prep later

●        Avoid costly rework

●        Signal operational maturity to investors and regulators

At The Sugar Water Operations Team, we help lean teams plan for eCTD without overspending or overbuilding. Our strategic approach ensures you're ready when the time is right—with a plan to get the tools and support you need when you need them.

📩 Not sure if your team is eCTD-ready? Let’s chat. Our checklist-based assessment can help you see what’s missing—before it becomes urgent.