Second Brain Folder Structure: Notes Your AI Can Find

A useful second brain folder structure gives incoming notes, original sources, active projects, reusable explanations, and archived work a clear home. Start with a few broad folders and a short index for each project. fenbs can hold the current decisions and checkpoints outside that archive, giving connected assistants a reliable starting point for active work.

A folder name helps you locate a note; it cannot tell you whether the note is accurate or still applies. Add a purpose, source reference, and status where those details matter. The structure below is a starter you can adapt in a Markdown editor, including Obsidian, without building a complicated filing system.

What should the starter folders contain?

Create one top-level folder for the collection and a small number of folders beneath it. Markdown means plain text with simple formatting marks for headings, lists, and links. Obsidian’s storage documentation↗ (opens in a new tab) explains that its vault is a local folder containing Markdown notes and any subfolders, so this example can also serve as a vault.

second-brain/
  00-inbox/
  10-projects/
    workshop-proposal/
      index.md
      questions.md
  20-sources/
    community-survey.md
  30-notes/
    evening-access-needs.md
  90-archive/
  attachments/
  start-here.md

The numbers only keep the list in a predictable order. Incoming material goes in the inbox until you decide whether to keep it. Sources retain the reference and your reading notes. Reusable notes contain your own explanation of an idea, while a project index gathers the material needed for a particular outcome.

Write the folder rules in the start page so you do not have to remember your original reasoning. The broader second brain introduction explains what belongs in a knowledge collection; the job here is to give those materials stable locations.

How should you format a source note?

Keep the source’s identity separate from your interpretation. A source note should let you return to the original and find the relevant passage. Give it a descriptive filename, then record the author or organization, title, original link, date when relevant, and page or section you used.

# Community survey: workshop scheduling

Source: [Original report](https://example.com/report)
Organization: Example neighborhood group
Relevant section: Scheduling questions
Status: Read; sample limitations still need review

## Why I saved it
Supports the scheduling discussion for the workshop proposal.

## My reading notes
Record what the source actually says and where to find it.

## Limits and questions
Which residents were not represented?

## Used in
[Workshop proposal](../10-projects/workshop-proposal/index.md)

The sample report address is a placeholder for your own source. Replace it before relying on the note. If you quote material, mark the quotation clearly and keep its location; put your interpretation under a different heading. Do not let a concise summary erase a qualification that changes the meaning.

Store attachments in the attachment folder with filenames you can distinguish. A scan called “document” becomes hard to recognize later. Keep the reference to the original location even if you are permitted to retain a local copy, and include the version when the document can change.

What belongs in each project index?

A project index is a short map to the notes needed for one result. Write the goal at the top, followed by a few links with explanations. For a workshop proposal, that might mean the application requirements, scheduling survey, venue questions, and your current draft.

• Outcome: what this project will produce and how you will recognize completion.
• Sources: links to the evidence, with a sentence about what each source supports.
• Working notes: explanations and alternatives that are still being developed.
• Current work record: where approved decisions, task progress, and the next step are maintained.

Keep source notes in one place and link them from several projects if needed. Copying the same summary into multiple folders creates several versions to correct. For active work, fenbs keeps current context beside the tasks; the index can point you there instead of becoming a second task tracker.

Should you use folders, tags, or links?

Use folders for broad homes, links for specific relationships, and a few tags only when they solve a recurring search problem. A folder tells you where the note lives. A sentence containing a link can tell you why two notes belong together.

For example, write “The scheduling argument depends on the community survey” and link to the source note. That is more informative than giving both notes a general workshop tag. Keep titles descriptive enough to recognize without opening every file.

Obsidian supports both Markdown links and wikilinks↗ (opens in a new tab). Its documentation recommends Markdown links when interoperability matters and notes that block references are specific to Obsidian. The starter above uses ordinary Markdown file links so the relationship remains readable in other editors. Test your links after moving files, because another app may handle paths differently.

For a full tool workflow, use the Obsidian setup guide. You do not need that tool or its graph view to benefit from a short index and clear source notes.

When should you move material into the archive?

Archive project-specific material when the effort is finished or deliberately paused. Preserve a closing note that says what happened, where the final output lives, and why the project stopped. A folder labeled “old” gives less help than an index that clearly describes a completed proposal.

Do not move a shared source just because one project ended. The same survey may still support another active project. Keep reusable source and explanation notes in their usual locations, and archive the project’s own drafts and index. Check the index links after any move.

Review the inbox during a regular work session. File useful notes, delete material you no longer need, and leave a next action for items that require reading. If the inbox keeps growing, reduce what enters it before creating a more elaborate set of folders.

How does an assistant know which notes to use?

An assistant needs actual access and an explicit starting point. A folder on your computer is not automatically visible to an AI app. Use the app’s supported way to provide selected files or connect an approved tool, then state which project index and sources matter to the current question.

The AI second brain guide covers using saved knowledge with assistants; the AI brain guide explains the smaller record of current work. Ask the assistant to distinguish archived options from current decisions and to name missing evidence before it fills in a gap.

How to do this with fenbs

1. Create a free account and add the project represented by your active folder. fenbs is free for one person, no credit card.
2. Add current tasks and an AI context note stating the goal, important source locations, and unresolved questions. Keep long Markdown notes in your notes collection.
3. Add reviewed references to Links and listings and record the choices a person approved in Decisions and rules.
4. Connect a supported assistant through Integrations. Ask it to read the context before working and save progress, remaining checks, and the next step afterward.

fenbs is not the right fit for storing an entire Markdown vault or exploring a note graph. It does not automatically import your folders. Use it for the active work record when that record needs to stay available across supported assistants.

Before expanding the structure, try a retrieval test. Find the source of one claim, locate the current project index, and explain the next step without opening every draft. Fix the specific failure you encounter. The second brain collection can help when a more specialized workflow becomes necessary.