How do I delete unlinked folders from iCloud.com
On new iOS, you can use the files app to navigate and delete these files. 


https://support.apple.com/en-us/HT206481


Before that app shipped, there wasn't a file browser on iOS and Apple didn't expose that functionality to users.

There is a file browser on OS X, but the "truth" for App Folders is currently stored in iCloud, so you can't delete a folder on OS X and have it stay deleted. The bird daemon will re-download the folder from the cloud if you try. The developer that created those folders will have to implement a clean up routine (similar to how 1Password allows you to instruct the app to delete iCloud data and the program itself removes the data).

If you created the folder or document from OS X, then you can drag that folder to your desktop (or elsewhere) and you'll be notified of the pending 
deletion from iCloud.



Pay attention to the kind column to determine if you need the App to delete things or if you are trying to delete a normal file or folder. For more information you can use the command brctl log --wait to see status, minor errors and warnings of the iCloud folder and file syncing from OS X using terminal.app.