The best option you've got is running an online scan. Otherwise, you might wanna try disabling the autorun feature on all drives and manually deleting the .exe files using the command prompt. If they are write protected, just try this in the command prompt:-
attrib -r -a -s -h <filename.exe> (Enter the filename without the "<" and ">").
After this, use the del command. This is a long process, but an alternative one.