Note: I don't have BitTorrent, so there might be an easier way to do this.
As far as I understand it, BitTorrent allows others to download files from your computer, so the BitTorrent Program is the one using the files.
Here's a surefire way to do it, but it's a bit complex:
Start Your Computer In Safe Mode:
Instructions for starting in Safe Mode
Then delete the files!
If you're using msconfig, you'll need to change the settings back to normal or else it will keep booting in safe mode.
If you have any questions, email or IM me!