I had a problem of shortcut virus in mu USB flash drive. i was worry about that because it convert my all folder to shortcuts. then i find the solution of this problem. and thought that may be you also have this problem. so i have discovered a command for CMD. just write this command in CMD and your virus will be removed.
attrib -h -r -s \s \d g:/*.*
Note: Replace g by your drive name from which you want to remove the virus.