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I'm pretty sure it's the "New Folder.exe" referenced above. How can I get my files off without carrying the infection along with them?

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Which "'New Folder.exe' referenced above"? What operating system do you run? – slhck Sep 16 '13 at 19:10
use a linux live CD if you ARE SURE it is a kit doing the mess and not a real virus. then, format the usb stick and place the files back. – Lorenzo Von Matterhorn Sep 16 '13 at 19:22

You haven't provided much information, so the only thing I can suggest is to scan it with any antivirus/antimalware software to remove the virus. I highly recommend Malwarebytes Anti-Malware (there is a free version available).

Other files will remain in the flash drive.

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