What error does it give you when you try any of the things you mentioned? And, have you tried renaming them first? Also, did you try stopping the FTP service first, and then deleting them?

Also you may want to check that you have denied your users to the ability to change permissions on the folders. If you have not done so, they can change permissions by relatively simple FTP commands rendering them inaccessible to you. Check your FTP's permissions on all files and folders to see if you still have the appropriate permissions, then go into the security setting for them, then go into "advanced", then disable "change security settings".
 
If you have been denied access to these files, simply go in and change the permissions back to allow you access (may need to be an administrator to do this).