I can't figure out how to make a file permanently "un-hidden"

So this is the story. My wife downloaded a virus that I couldn't fix on the PC. I thought it was a good excuse to move to mac for good. So I bought a Mac Pro and am running Lion. The problem is that the virus made the music and movie files on my hard drive "Hidden Files" I have been able to see them throught the help of the program "Houdini" as well as the comand line instructions found in the forums. But I haven't found a way to make the files on my external drive permanantly "visable". Is there away in OSX 7.3 to do that? I have looked and looked but found nothing online or in support forums. Again I am just looking to make the files i the external USB drive visable. I also want to add that I have two drives and that simply transfering them to the other drive by dragging the root "Music and Movies" folder didn't work. They still show up on the new drive as being "Invisable"
Thanks for any insight anyone may have!
-TVFrog

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I can't figure out how to make a file permanently "un-hidden"

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