Is it safe to scan and clean an external hdd of malware/virus on an otherwise clean system ie my system!?
Does the antivirus software on my machine do it's work externally? ie if a virus is detected does it quarantine the object to somewhere on the external hdd rather than onto my machine?
Would using a separate user account for this work be of any benefit? Thanks.
Are you sure tour system doesn't have an application that scan or index new devices? Like a media player that tries to extract metadata from multimedia files.
I would recommend booting from a live CD or live USB in read-only mode, not mounting your partitions, and disconnected from any network. After that load [a VM with] your antivirus, then mount your external drive and check it. However, this will not prevent a rootkit from infecting your BIOS and you will have no guaranty that your antivirus found all the malware. It's still better than nothing.
If you want a bullet proof method to remove your virus from the drive, the only way is to destroy it. Erasing it is not enough, as its firmware could be infected.
First of all always use a virtual machine instead of your installed OS and mount it in read only mode when doing something with (probably) infected externals!
This prevents your PC/Account from being infected by whatever is on this HDD. Most likley a usual anti-virus should then be able to detect most of the malware and delete it.
If you doubt it anyway you can completely wipe the HDD using the VM.
In addition, there are already posts on this topic:
