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When I use my USB drive on Windows computers, then return to my Linux computer, I find many extra files are added to the drive, often exe files and various folders.

  • Is it sufficient to delete the new files? Will some viruses be placed inside my files?
  • Is there some software to help identify and delete these, from Linux?
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2 Answers

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There is also the possibility, that any malware install itself in the MBR/VBR boot sectors of the drive. From there it could be executed automatically if booting from USB storage devices is enabled.

As soon as the malware runs, it could install nasty root/bootkits.

To clean the MBR of the usb drive from any malware, install a new one. And remove any existing bootflag from all partitions on the drive by using fdisk or any other partition manager (gparted, cfdisk, ...)

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  1. Yes, unless a virus appends itself to an exe file.
  2. Try ClamAV, an open-source virus scanner which runs on Linux.
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Appending code to existing executables is an incredibly common technique. Just search for "virus append exe", there's gobs of them out there to eat you. – Mat Feb 26 '12 at 9:22
That's quite interesting... editing my post to reflect it. – Renan Feb 26 '12 at 14:59

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