OK - I have heard of malware playing this game with core sys files, but not with personal files manually tucked aside. Is feasible you've transferred across an infected file across, but wouldn't have thought would have cloaked your external drive... but anything is possible. If this IS the case, DO NOT TRANSFER ANYTHING OUT OF THE DRIVE JUST YET!!
(Oh, and yes discussing various software apps is A-OK, so long as not going into illegally obtaining or cracking BTW

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First, download BOTH
Ad-Aware and
MalwareBytes - the two apps I'd trust to strip out any malware. Install (don't run a scan yet if given the option) then continue reading.
Now both these apps are at their best when OS has been loaded up in safe mode. Can either reboot and tap away at the F8 key before the Windows boot-logo arives. Simpler yet - hit WinKey+R and enter
msconfig. Go to the
boot tab and select "Safe Boot".
Taking this second option means that if after running one scan and needs to reboot so you can run other utility, will bring you straight back to safe mode without beating the F8 key. Just remember that when you are ready to boot as normal, go back into msconfig and rest your boot option. Both utilities should be run as Admin for extra gusto.
Now that everything has been scanned and stripped, first open up Folder Options from Control Panel (or if XP, go to the View option on the menu bar and open Folder Options from there). Make sure Hidden files and System files are both visible. Next, open up the HDD in My Computer. Right-click on each of the ROOT folders, and make sure each is neither set as Hidden or System. If running Vista, go to Advanced options and allow indexing.
HOPEFULLY this should sort things out. As I said earlier, don't try and copy anything off till you know all files are clean.
As to AV/Security apps?? I really like Symantec Endpoint Protection, but that's corporate ware. DECENT free options -
Avira,
Nod32 or
Comodo all good. Paid for -
G Data has had blazing reviews the last year or so,
Panda, or
Avast. Personally I steer to either Endpoint or Comodo (as Endpoint not yet 100% on Win7
yet) as they are by far the two most light weight suites with bundled firewall
and system protection, but then everyone will have their own opinions.
PLEASE PLEASE PLEASE stay the hell away from either AVG or McAfee - They are the two BIGGEST heaps of crap on the market. Trend Micro isn't much better either. Have a look
here for a few options to check out. Also check here for another
independent comparison.
Hope this all helps