You can't run anything on a external drive like it was a separate computer, it has to be connected to a computer to run the commands to clean it. I am not sure what your using, but here are the basics I would do first off:
Remove whatever AV your using and go to www.filehippo.com and download AVAST! or AVG and do a full system scan - this repeatedly has resolved alot of people issue relying on MS Essentials. Do FULL SCAN, not a quick scan on all drives listed (this would include the 'infected').
Download Malwarebytes do a FULL system scan (AV doesn't pick up alot of malware) - this resolved almost ALL other similiar posts to date as most had Malware the AV didn't pick up. Again also include the external drive.
Repeat the AV/Malware scans till the system comes up clean.
Did you install all Windows Updates? Including options except BING? Check them and repeat till ALL are installed, these are the FIXES to protect your PC form being infected too.
Download and run Slim Drivers, install all the latest updates but you don't need to reboot until you do the last update. These also, as software, have been found to be ways to be 'infected' and will patch any of the potential security holes.
As for your comment about "backups"; are you talking backups of your computer you made THAT are infected? If so, then you can manually delete those by just deleting the WindowsImageBackup directory.