Why I Deleted So Many Folders in Obsidian—and What I Learned

4 minute read

Why I Deleted All My Obsidian Project Folders After 3.5 Years of Note-Taking

For years, the digital knowledge management community has debated how best to organize notes. Should you use tags or connections? Folders or MOC (Map of Content) notes? Which is more efficient?

After using Obsidian for over 3.5 years, creating more than 6000+ notes, I’ve come to a realization that might sound counterintuitive: folders became a mental burden. In this post, I’ll share why I deleted all my project folders and what I do now instead.

My Early Setup: One Folder for Each Project

During my PhD, I managed a growing number of research projects. To stay organized, I created a parent folder called PhD inside my Obsidian vault. Within that, I had over 20 subfolders—one for each individual project. Some were completed, some abandoned, and some still ongoing.

Later, when I started my full-time research job after completing my PhD, I continued the same structure under a new Job folder. Before I knew it, my vault had a deep hierarchy:

Projects
  ├── PhD
  │     ├── Project 1
  │     ├── Project 2
  │     └── ...
  └── Job
        ├── Project A
        ├── Project B
        └── ...

You might be thinking—why did I create so many folders? The original idea was simple: make it easier to share notes with others later, or even publish parts of it. It was almost philanthropic. But that mindset didn’t age well.

The Problem with Folders: Mental Walls

Over time, I noticed something was off. Folders started to feel like walls in my second brain.

Every folder acted like a separate room. When I had an idea or insight, I subconsciously asked myself, “Which room does this belong to?” That tiny hesitation created friction. Instead of freely connecting ideas across projects, I found myself restricted by folder boundaries.

I often had to merge notes from different folders just to understand overlapping ideas. That meant digging, copying, linking—and wasting time. These mental walls defeated the whole purpose of digital note-taking, which (for me) is:

Reusing notes across papers, projects, and reports
Finding and understanding a note in 5 seconds
Being productive and kind to my future self

Folders were killing all three goals.

My Aha Moment: Open Floor Collaboration

Think about how many modern tech companies embrace open office plans. One reason is that physical walls reduce communication. In contrast, open floors lead to spontaneous conversations, quick idea exchanges, and unexpected collaborations.

That’s exactly what I wanted in my second brain.

So, I deleted all my PhD and Job folders and created a new parent folder: Research.

All of my notes, from every past and current project, now live inside that one folder. There are no subfolders—just notes floating in one open space.

It feels like all my research notes are now working together in an open-floor tech company—seeing each other, helping each other grow, and generating new ideas effortlessly.

How I Stay Organized Without Folders

Now you might wonder, “Without folders, how do you keep track of different projects?” Great question. I use MOC notes (Map of Content) for each project. For example:

MOC PhD: Links to all notes related to my PhD work
MOC pySynphasor: A hub for my open-source project pySynphasor

Each MOC note acts like a dashboard or landing page for that project. It holds links to relevant notes, todos, and summaries. This allows me to organize without rigid boundaries.

Did I Lose Anything by Doing This?

Yes—my initial goal of “philanthropic sharing.” 😅
But in return, I gained something far more valuable: freedom of thought and creative connection.

Now, I can search, find, and connect notes across time and context without mental friction. My knowledge system feels alive again.

🧠 Final Thoughts

If you’re using Obsidian or any note-taking system, I encourage you to ask:

Are your folders helping or hindering you?
Is your setup maximizing reuse, recall, and connection?
Do you need separate rooms—or one open space with smart maps?

For me, deleting folders was a breakthrough. Maybe for you, it could be the next step toward building a more connected second brain.

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👋 About Me

Hi, I’m Shuvangkar Das — a power systems researcher with a Ph.D. in Electrical Engineering, currently working as a Research Scientist. I work at the intersection of power electronics, inverter-based DERs (IBRs), and AI to help build smarter, greener, and more stable electric grids.

My work spans large-scale EMT simulations, firmware development, reinforcement learning, and hardware prototyping. Beyond engineering, I’m also a YouTuber and content creator — sharing hands-on insights on productivity, research, and knowledge management. My goal is simple: to make complex ideas more accessible and actionable for everyone.

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