If you have some virus on your pen drive   that hide your some or all file in your drive. You can get back your file again by follow this process.

Click on right button to My Computer>>click on properties>>system restore>>click on turn off system restore on all drives>>click on OK

New window will come>>click on yes

Click on tools of my computer menu bar>>choose folder option>>click on view>>click on show hidden files and folders>>unmark the hide extension and hide protected>>click on OK.

Now you will find your folder in hidden state. (((Only for windows xp)))

Process for windows 7, 8, vista, xp (((http://imacify.com/2011/02/how-to-recover-hidden-files-from-virus-infected-usb-pendrive/)))