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I scanned my flash drive for viruses using avast free. It didn't found a threat. But it said that there are files that couldn't be scanned. How do I delete those files? I can't see it even if I set to show hidden files. Can those files cause harm on my computer?

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There's a pretty good chance that you have a rootkit on your PC. Set explorer to show hidden files (see Moons answer), if you still can't see them, navigate via the command line to the folder, and run dir /a, does it list the files? – Bobby Jul 21 '10 at 6:38

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Set up your PC to "Show Hidden Files" and Unhide Protected System Files by deselecting "Hide protected System Files" from Tools>Options under the View Tab..

then delete all the files you want...

if you get any messages like Unable to delete or access denied... restart in Safe Mode and proceed...

and if you don't want to restart in safe mode and your unable to delete because of error messages then

Open Task Manager... kill Explorer.exe.... press 'Win + R' type in cmd and press Enter to open command prompt and then use Dos commands to go and delete the files.. this

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You might be better off just formatting your flash drive. Go to My Computer, right-click on the drive, and choose "Format". Do a full format, not a quick format. Everything on the disk - including any hidden files - will be completely erased, so make sure to back up any files from the drive which you will need later.

What types of files is it saying can't be scanned? You may be able to have them show up when using the command prompt. Try typing dir /A:H path, dir /A:S path and dir /A:HS path, where path is the path of the folder with the files in it. It should show you any files which are hidden (first option), system-hidden/super-hidden (2nd option) or both (3rd option).

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this can only be done in a flash drive which you dont have data that is required... but normally we dont do like that. Anyway aware that it removes off everything. This solution may not be fit for everybody. – thegeek Jul 21 '10 at 6:16
That's true. However, in this case, it would work to copy the files which need to be kept to somewhere else, then restore them once it's been wiped. Flash drives are usually small enough that reformatting works. If it were a regular hard drive, I wouldn't recommend it. – nhinkle♦ Jul 21 '10 at 6:20
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Try connecting it with a Linux system.

And then you can play with it, without any issue ( bcoz virus cannot harm your Linux system !! ). Like listing out all files, using 

ls -l
find . -type f

And then remove only the unwanted files even it is full of spaces or special characters, by using find command with rm.

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