3 ways I organize my PhD notes

TL;DR

Use folders to separate clutter-prone items (like PDFs and bibliographic citations) from atomic knowledge notes, not to force arbitrary topic boundaries.

Briefing Cornell Notes

Briefing

A growing Zettelkasten in Obsidian can quickly become “mentally squeezed”—not because note-taking stops working, but because the sheer volume makes it hard to find what matters next. Morgan’s practical answer is to build an entry point into that expanding knowledge using three Obsidian tools—folders, tags, and structure notes—while keeping the core Zettelkasten linking process as organic as possible.

Folders, in Morgan’s workflow, aren’t used to categorize ideas by topic (like “juggling as sport” vs. “juggling as art”), because that forces arbitrary boundaries between notes that naturally connect across subjects. Instead, folders serve as a clutter-control mechanism: they separate “special” materials from the main knowledge graph. In a sample vault, two top-level folders—“sources” and “files”—hold bibliographic notes and referenced media (PDFs and images). Source notes store citations (for example, an MLA-cited reading such as “How to Take Smart Notes”), while the “files” folder keeps the actual documents. Notes can then link to these items without mixing PDFs and citations into the everyday atomic-thought space.

Tags come next, but with a similar restraint: Morgan avoids tags as a primary way to group knowledge because tags can feel like imposing categories that don’t emerge from the notes themselves. Searching and linking already provide topic discovery. Still, tags are useful for operational tracking—especially when the system grows large. Morgan uses a tag pane to keep certain tags visible at all times. In her setup, a “pencil” tag marks items that still need work (e.g., a book like “Vibrant Matter” has been read but hasn’t yet been turned into notes inside the Zettelkasten), while a “link” tag flags notes that exist but haven’t been interconnected with the rest of the network. Clicking those tags surfaces which notes are pending, turning the tagging system into a lightweight task reminder rather than a conceptual taxonomy.

The real organizing breakthrough is structure notes—what Nick Milo calls “maps of content.” Instead of tagging or foldering every note by theme, Morgan creates dedicated “structure” pages (marked with a “house” tag) that act like an index or table of contents. For example, a “knowledge” structure note gathers all notes related to knowledge and ways of knowing, then subdivides them into thematic sections such as metaphors for knowing (including sight and feeling metaphors). Importantly, Morgan builds these structure notes bottom-up: she lets notes accumulate freely, watches where themes pool, and only then organizes them into structure notes. This creates a stable entry point for writing—when it’s time to draft, she can open the relevant structure note and choose which sub-area to focus on.

Morgan’s broader message is that organization should reduce stress without constraining thinking. Folders and tags manage practical clutter and workflow gaps; structure notes provide navigation once the knowledge base becomes too large to browse casually. As the dissertation grows, the structure notes evolve too—new topics become new maps, rather than forcing the system into pre-decided categories.

Cornell Notes

Morgan’s Obsidian Zettelkasten workflow tackles the “mental squeeze point,” when too many notes make the system hard to use. She uses folders mainly to keep sources and attachments (PDFs/images) from cluttering atomic notes, not to impose topic boundaries. Tags are reserved for practical reminders: a “pencil” tag flags readings that still need notes, and a “link” tag flags notes that exist but haven’t been connected to the rest of the network. The main navigation layer comes from structure notes (maps of content), marked with a “house” tag, which function like an index/table of contents. Structure notes are built bottom-up from where themes naturally pool, giving a clear entry point for dissertation writing.

Why doesn’t Morgan rely on folders to categorize ideas by topic (e.g., “juggling as sport” vs. “juggling as art”)?

She calls that split arbitrary because notes often connect across boundaries. A note about “juggling as a hobby” might link to “skateboarding as a hobby,” which wouldn’t belong in a juggling-only folder. She also finds that topic folders don’t solve the underlying mess unless the folder system is extremely systematic, so she uses folders instead to quarantine clutter—like bibliographic sources and attachments—while keeping the knowledge graph itself free to connect organically.

How do folders function in her sample vault, and what’s the difference between “sources” and “files”?

In the sample vault, “sources” holds bibliographic notes (e.g., a note containing an MLA citation for a book such as “How to Take Smart Notes”). “files” holds the actual referenced documents like PDFs and JPEGS. Notes can reference these items via hover previews, and she notes a workflow trick: putting an exclamation point in front of a PDF filename embeds the PDF directly inside the note.

What role do tags play, and why does Morgan avoid using tags as a primary knowledge taxonomy?

Tags group items around a topic, but Morgan doesn’t like using them to force conceptual categories onto notes. She prefers organic connections through Obsidian search and linking, especially since she expects hundreds of juggling-related notes. Instead, tags act as operational markers. She uses a tag pane to keep certain tags visible and clickable so she can see what still needs attention.

What do the “pencil” and “link” tags mean in her workflow?

The “pencil” tag marks notes that still need to be created. For example, she has a book (“Vibrant Matter” by Jane Bennett) that she read earlier but hasn’t yet been turned into Zettelkasten notes, so the pencil tag reminds her to add atomic thoughts. The “link” tag marks notes that already exist but aren’t yet interconnected with the rest of the Zettelkasten. Clicking it shows which notes still need connection work.

How do structure notes work, and how are they different from tags?

Structure notes are dedicated pages that organize other notes under a navigational “map of content.” They’re marked with a “house” tag and behave like an index or table of contents. Unlike tags (which group notes by labels), structure notes are built around a topic page (e.g., “knowledge”) and then subdivided into sections (like “metaphors for knowing,” with subsections such as sight and feeling metaphors). Morgan builds them bottom-up after themes emerge, rather than deciding categories first.

What’s the bottom-up principle Morgan uses to create structure notes?

She first allows notes to accumulate freely, letting ideas pool naturally. Once she can see where themes are forming, she creates structure notes to gather and navigate those clusters. If a section grows large (e.g., metaphors for knowing), she may create another structure note to further map that subtopic. The goal is to reduce overwhelm without restricting what she can note in the first place.

Review Questions

When does Morgan prefer folders over tags, and what problem is each tool meant to solve?
How do “pencil” and “link” tags change the day-to-day maintenance of a large Zettelkasten?
What bottom-up signals tell Morgan that a new structure note (map of content) is needed?

Key Points

1
Use folders to separate clutter-prone items (like PDFs and bibliographic citations) from atomic knowledge notes, not to force arbitrary topic boundaries.
2
Avoid using folders to categorize ideas when notes naturally connect across themes; instead, let linking handle cross-topic relationships.
3
Reserve tags for operational workflows (e.g., reminders) rather than building a rigid taxonomy that may conflict with organic connections.
4
Turn on Obsidian’s tag pane (via core plugins) to keep key tags visible and quickly actionable as your note base grows.
5
Use structure notes (maps of content) as navigation layers—like an index or table of contents—so writing has a clear entry point.
6
Build structure notes bottom-up: accumulate notes first, then organize only after themes become visible.
7
Expect structure notes to evolve over time as new dissertation needs and new clusters of ideas emerge.

Highlights

Morgan’s “mental squeeze point” is solved less by taking fewer notes and more by adding navigation: structure notes provide an entry point when browsing becomes stressful.

Folders aren’t for topic taxonomy in her system; they’re for quarantining sources and attachments so the knowledge graph stays clean.

Tags become maintenance signals: “pencil” marks missing notes, while “link” marks notes that exist but haven’t been interconnected.

Structure notes act like an index/table of contents and are built bottom-up from where themes naturally pool, not from pre-decided categories.

Topics

Mentioned

Morgan
Nick Milo
Jane Bennett