After finishing up school, I'm transitioning away from my school-run IMAP e-mail account. During my time, I managed to save thousands of messages in dozens of subfolders in my "Inbox" hierarchy ...

It will be far easier for you to have a folder tree, and inside the folders, your media files which would be rated and renamed.

Use Terminal to see an indented tree-like view of a given folder’s structure.

Download, install and run Fast Duplicate File Finder (link in Resources). Click the "Add Folder" button. Check the external hard drive on the Browser For Folders tree list.

Poof! With that weird folder finally zapped out of existence, I went back to the top-level folder and performed a simple shift-delete, wiping the entire folder tree out of existence.