Filamental and Obsidian can point at the exact same folder. Open an existing Obsidian vault in Filamental as it is, or open a Filamental project in Obsidian as it is, either direction works, and opening a folder in one app never locks it against the other.
This is separate from the Obsidian Plugin: that's a viewer inside Obsidian, this is two apps sharing one folder of real files.
It happens once per note, when Filamental first takes that note in, and never again after that. A Note Name you type later stays a plain clickable link, and Obsidian never turns anything into connectors.
Import from Obsidian is the way to do it for a vault. You'll find it under Obsidian in the New / Open / Import… window (see New, Open or Import), and Filamental offers it when you open a folder it recognises as a vault. Import reads your vault's wikilinks and any front matter relationships and turns them into real connectors, keeps the fields your notes already have (tags, aliases and the rest), and lists any links that point at notes that don't exist.
If you open a vault as a plain folder instead, Filamental takes in only the notes that have no front matter yet, adding its details and turning their wikilinks into connectors the same way. Notes that already have front matter of their own aren't taken in that way and won't appear as nodes, so for a vault the import is the better way in.
Either way, the connectors arrive untyped on purpose, since Filamental can't know whether one note supersedes another, contradicts it, or just happens to mention it, and guessing would be worse than leaving that decision to you. Run it once, then type the connectors that matter. The import can also use your vault's top-level folders as classifications, so the notes arrive already sorted.
Works best on a moderate-sized vault. A huge tangle of links will naturally "ball up" visually once it's all sitting in Filamental's physics, so a very large or densely cross-linked vault is worth importing in stages, or just left readable side by side rather than imported at all.
Plan and build a project in Filamental while it's still moving, then archive it into Obsidian once it's settled.
Filamental is where a structure is still being worked out: the 3D layout, AI reading and writing it live, connectors you haven't fixed the shape of yet. Once a piece of work is finished, dropping it into your Obsidian vault folds it into the permanent library you already keep there, alongside everything else you've settled.
Nothing forces the move. Leave a project in Filamental as long as you like, or read the same folder in both apps side by side for as long as that's useful. The workflow above is just the one that fits how most people already use two note tools together, not a rule either app enforces.
Both apps can be read by AI, but they suit a different moment in the same workflow. See AI Connections & Prompting for the full picture, the short version here is about which folder to point at, not how to connect.
While a project is still moving, Filamental is the active resource worth a live connection, MCP or Filamental AI, because it's what's actually being read and rewritten as you work rather than something sitting still.
Once you've archived into Obsidian, that folder becomes reference material rather than a live workspace: folder access or a skill will still read it exactly as it reads any other Markdown, but nothing is restructuring it any more.
Point AI at whichever matches what you're doing: build and reason against the active project, look things up in the archive.
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