Invisible directories

Hello,
I had a laptop that was infected with a lot of viruses a few days ago.I was going to download a virus removal tool because I couldn't install an antivirus.Before doing that I wanted to backup my files so I inserted my external HDD and it got infected too!! When the laptop was clean,I simply scanned my HDD and it was cleaned too,but now all my folders had disappeared though the drive space was still occupied.I can manipulate the folders only in DOS but can't even view them using windows.What can I do to make my files visible in normal windows again??? I'm running Windows 7.
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More about invisible directories
  1. Make sure they didn't get changed to hidden folders. Here is a link to show you how to view hidden files and folders.

    http://www.bleepingcomputer.com/tutorials/tutorial151.html
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