Just insert your pen drive in the USB port, now a autorun window(usually it includes Open to view Files and
Take no action options) will open to choose the program that will run your pen drive but just ignore it by clicking the Cancel button right after the OK buttonNow go to Start -> Run.. and type cmd to open the Command Prompt window. Now go to My Computer and Check the Drive letter of your USB drive or Pen Drive.(If it is written Kingston(I:), then I: will be the drive letter)
In the Command Window(cmd), type the drive letter(as above is I:) and now hit enter. Then type the dir/w/o/a/p and Hit Enter

Now you will get a list of files that are in your pen drive. In the list, search if anyone of the following do exist.

1. Autorun.inf
2. New Folder.exe
3. Bha.vbs
4. Iexplore.vbs
5. Info.exe
6. New_Folder.exe
7. Ravmon.exe
8. RVHost.exe or any other files with .exe Extension.

If you find any one of the file names as above, Run the command attrib -h -r -s -a *.* and Hit Enter. Now Delete each File using the following Command del filename. Now just scan your USB drive with the anti virus you have to ensure that you made your Pen Drive free of Virus :D