Usually there are hidden folders which contain your files, cut them and paste at secure location like in your computer and delete those hidden shortcuts and hidden folders.
Open command prompt and run as administrator.
Usually such files are marked with attribute : hidden, read-only, system files.The files in root are usually of the names autorun.inf, newfolder.exe, regsvr.exe and more. Now a days every Computer user has came across a pen-drive that is badly affected by a virus that creates shortcuts in pen-drive and hides the rest of the file after creating autorun.inf in the root of pen-drive or USB removable disks.
