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It should work fine. They usually scan for all viruses. I have found a few windoze bugs on my machine and I don't have windoze. As long as the drive or partition is mounted, it should work.
Note of caution: If you have NTFS, I would mount as read only. They support writing but, big but there, I have read of people messing up when writing data to NTFS. It has been a while since I read any of those but be careful at least.
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