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Depends on the virus - there are different ways to remove things depending on what the virus payload is. In general, however, you should remove viruses via a boot CD; that way mounting the USB drive won't harm the OS.

A script itself would be of limited use because viruses are very different, so you would have to customize the script for different viruses.

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Q: How do you write a script in Ubuntu to delete a virus in a USB flash drive?
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