This error may occur because there are hidden files/folders under the directory you are trying to delete.  Lets say you have a directory named "test" and you cannot delete the directory and get the following message from your FTP Client

Command: RMD test

Response: 550 test: The directory is not empty.

**This Commonly happens if you are using Front Page.  Front Page inserts hidden "_vti_" folders under each directory it creates.

If you are using "Filezilla" as your FTP client, you may do this to be able to delete the directories that contain other hidden files or directories in them:

Click on the "Server" menu and select "Force Showing Hidden Files"  Click "OK" on the dialog Box when it appears.

-All steps complete, if you still cannot delete folders after this, reconnect your FTP client, if you still cannot, right click an empty area on the Filename column on the Right-Hand Side. and choose "Refresh" and try again.

NOTE: If you are not using Filezilla, please refer to your FTP Client's documentation on how to enable it so it detects and shows hidden files/folders.