To find duplicate files, create a Smartlist by pressing F9.
On the 'Edit Smartlist' dialog, type 'Possible Duplicates' for the name.
Click the 'Import / Export' button near the bottom and enter exactly this text: ~dup=[File Size],[Name]
Then click 'OK' twice. You will be viewing a list of files where the name and the file size match.
You can mouse-over and view the tooltip or use Action Window > Tag to see more information about the files.
Select any extra files (ctrl+click) and press 'Delete' to delete them. You probably want to send duplicate files to the 'Recycle Bin'.
You can use 'Edit' at the top of the Smartlist to filter to only a particular media type, or to change the fields it checks for duplicates. An example of a similar Smartlist to help find audio duplicates of different formats is: [Media Type]=[Audio] ~dup=[Name],[Album],[Artist],[Track #]
Another Possible Solution
If your drive shows up as E: one time and then F: another time, for example, it would look like two different drives. Windows does that sometimes. People get around it by assigning the drive to a high letter, like Z:
You can search for E: files and remove them by pressing the Delete key. Try a few before you do very many and verify that you're getting the results you expect.