Shortcut virus

yesterday, my external hard disk was infected with the shortcut virus. i cleaned it after connecting to my desktop. everything went fine. and through web, i came to know that it only effected usb powered stuff and not hard drives.

but my c was infected. just documents and settings. and some important folders into that. like appdata, roaming, etc.
i went online and searched and ended up deleting something in regedit.exe also I go to task manager everytime and delete the scrip.exe, because i see hidden folders randomly named like 131b popping up from nowhere and creating java script files.

now the problem is i cant run a single exe file. no matter what i click, windows asks me "open with . . ". even if its snipping tool, brower or anything. what should I do?

Shorcut virus. the new post. please ignore this.