Body
Questions
- How should I organize my folders for use with Claude Cowork or Claude Code?
- What is a good folder structure for working with Claude?
- Where should I put a folder I want Claude to work in?
- Should I keep my Claude folder in Documents so it backs up to OneDrive?
- What should I not put in a folder I connect to Claude?
- How should I name my files and folders so Claude understands them?
- How do I keep my originals safe while Claude works?
- Can I use the same setup for both Cowork and Claude Code?
Environment
This article gives folder and file best practices that apply to both Claude Cowork and Claude Code on a Bowdoin-managed Claude account. It is written for anyone, technical or not.
- Who: Students, faculty, and staff using Cowork or Claude Code.
- What: How to lay out folders on a current version of macOS or Windows 11 so Claude's work is safe, tidy, backed up, and easy to find.
- Not in scope: The step-by-step setup itself, which is covered in Set Up a Cowork Project and Choose a Folder and Set Up Claude Code and Choose a Folder in the Related Articles section.
Resolution
The big idea: Give Claude one tidy, dedicated folder to work in, never your whole computer. Keep that folder in your Documents folder so it is automatically backed up to OneDrive, and a little structure up front keeps your originals safe and makes Claude's output easy to find.
Start with one dedicated home-base folder in Documents
Create a single top-level folder just for Claude work, and keep everything Claude-related inside it. This is the only folder you ever connect, which means Claude can never reach the rest of your files. At Bowdoin, create this folder inside your Documents folder.
- Mac:
Documents/Claude Projects
- Windows 11:
Documents\Claude Projects
Why Documents: You can keep your Claude folder anywhere you like, but Documents is the easiest choice at Bowdoin. Most Bowdoin computers have OneDrive folder backup (Known Folder Move) turned on, so your Documents folder already syncs to OneDrive automatically. That means anything in Documents/Claude Projects is backed up to the cloud and available from OneDrive on any client you sign in to, with no extra setup. Cowork and Claude Code work with the copy synced onto your computer and do not reach OneDrive in the cloud directly, but the sync still gives you an automatic backup, version history, and cross-device access. To check or turn on folder backup, see Sync Your Claude Work to the Cloud with OneDrive in the Related Articles section.
Connect the folder, not all of Documents. Point Claude at your Claude Projects folder specifically. Avoid connecting your entire Desktop, your whole Documents folder, your Downloads, or the root of your OneDrive. The more you connect, the more Claude can see. Narrow is safer.
Give each project its own subfolder
Inside your home-base folder, make one subfolder per project or topic, and connect or start Claude Code in just the project you are working on that day.
Claude Projects/
Fall-Advising/
Grant-Report-2026/
Committee-Minutes/
A simple layout inside each project
Within a project folder, a light structure helps Claude find inputs and keeps its output separate from your originals.
Grant-Report-2026/
inputs/ ← source files you give Claude (read these)
outputs/ ← where finished files go
drafts/ ← works in progress
notes.md ← context and instructions for the project
Tell Claude the layout with a one-line instruction such as Read source files from inputs and save anything you create to outputs. In Cowork you can save this as folder or project instructions; in Claude Code you can put it in a notes.md or project instructions file.
Protect your originals
- Because your Documents folder syncs to OneDrive, you can restore an earlier version of a file from OneDrive version history if Claude changes something you did not intend. See Sync Your Claude Work to the Cloud with OneDrive in the Related Articles section.
- Put source material Claude should not change in
inputs/ and ask Claude to write only to outputs/.
- Cowork always asks before deleting, and Claude Code asks before changing files, but a cloud backup is still your best safety net.
What not to put in a connected folder
Keep sensitive material out of any folder you connect to Claude:
- Financial records, bank or card numbers, and tax documents.
- Passwords, keys, or credentials of any kind.
- Protected or regulated data, such as student records or health information, unless you have confirmed with Bowdoin IT that it is appropriate.
- Anything you would not want processed on Anthropic's servers. For guidance, see Data privacy on your Bowdoin-managed Claude account in the Related Articles section.
Name things clearly
- Use descriptive names, such as
advising-notes-fall-2026.docx, not doc1.docx.
- Start dates with the year for automatic sorting, such as
2026-08-15-meeting.md.
- Avoid near-identical names that are easy to mix up, and keep one clear final version rather than many ambiguous copies.
One setup works for both tools
This same home-base-plus-project layout works whether you use Cowork or Claude Code. In Cowork you connect the project folder; in Claude Code you start it in the project folder. Either way, the folder is the boundary that keeps Claude's work contained, and keeping it in Documents keeps it backed up to OneDrive.
Additional Help
If you need further assistance, you have several options:
- Bowdoin Bot: Chat with Bowdoin Bot directly from any KB page for instant answers.
- Phone: Call the Bowdoin College Service Desk at (207) 725-3030.
- In person: Visit the Tech Hub in Smith Union during business hours.
- Submit a ticket: Request assistance through the Service Catalog.
AI-assisted content: This article was drafted with the assistance of an AI writing tool and reviewed by Bowdoin IT staff for accuracy.