This is specifically for Ubuntu, but if you'd like to include a reply that'd help Windows users, please do.
I'm working on the suspicion that there's malware on my neighbour's laptop, desktop PC and a external HDD. I've scanned them with ClamAV and found nothing. It's suspected to be a Windows virus/worm or a boot sector virus, and the source of infection is another Desktop PC which I've scanned with ClamAV (from live Ubuntu) and found more than one virus and three worms. That PC had only Windows installed, so I suspect that all the malware was for Windows only (symptoms of infection was that the system would sometimes restart randomly or when booting or when reaching the Windows login screen). I used my pen drive on that system (before knowing it was infected, and used the pen drive on my neighbour's computers only in Ubuntu) and also used another friend's pen drive which when I tried opening with GParted on my neighbour's laptop, GParted just crashed, and in one instance ended up corrupting my neighbour's EFI partition. Just by opening the pen drive with GParted.
When my neighbour's desktop PC restarted on boot twice simultaneously and his laptop restarted on boot once, I suspected his computers were infected.
What was done:
Wiped entire HDD of PC with DBAN and reinstalled Ubuntu from a DVD.
Now I need to backup some large files from the Ubuntu laptop (which I suspect is infected, although ClamAV found nothing), onto a pen drive so that I can transfer it to the Ubuntu desktop PC.
Am working with the paranoid assumption that if there's a Linux worm in the laptop which antiviruses can't yet detect, then it'd copy itself into a new pen drive automatically if automount is enabled.
So the question is: Will it help to disable automount and manually mount the pen drive? Is there any chance there's a lesser chance that a worm could infect a pen drive if mounting is done manually? If no, then how can I safely transfer those 7GB+ files to the desktop PC from the laptop?