Run this in Command Prompt (Windows Key+R (winXP) or just the Windows key on higher versions, type cmd, press Enter) as Administrator (Instead of enter, right click and select run as administrator) under Microsoft Windows :

attrib -h -r -s /s /d e:\*.*                     -- For a entire drive, where e:\ is our drive

attrib -h -r -s /s /d e:\"My Folder"     -- For a entire drive, where e:\My Folder is the path to the folder where the data recides

The files & folders are generally inside a folder with whitespace as the filename Example E:\ \MyFilesAndFolders, you could try cd " " or entering the folder without a name to see your files 

Word of Caution :

• DO NOT STOP YOUR ANTIVIRUS TO STOP IT FROM CLEANING PEN DRIVES AUTOMATICALLY. It is possible to RECOVER most of your data after it cleans up your drive
• Format your pendrive / external drive after you recover all your data
• Do not try to recover executables or other files inside which Virus are known to reside (.exe, .dll, Font Files, Screensaver files, MS Office Macro Files etc)
  • Generally an infected computer harbours multiple unwanted executable pieces of code.
  • New Code / viruses continue to be written - Anti-Virus Programs look for patterns in code (from known & recently discovered malicious programs) and could be totally ineffective from the latest viruses in the wild
• It is generally safe to recover Images, Plain Text (.txt only. but not .doc/.docm etc)
  • Be cautious of executables (its common to see files as MYFILE.jpg.exe) wherein files have multiple extensions. It is the last extension that actually matters (which could be hidden)
  • Check for the actual extension from a terminal (command Prompt)
• Remember to Format the infect the computer and install everything in the following order
  • Format complete drive (all partitions - after taking a backup)
  • Install your Operating System
  • Install a Antivirus & Update it
  • Restart and update your Operating System (might involve multiple restarts. Update-restart-check for updates till there are no available updates)
  • Scan your data and copy it back
  • Scan your Program installers and install your programs one by one
  • Take a snapshot of your system which you can use later (just in case - this can save significant time)