How to correct the upgraded windows 7, when I launch a program it prompt me a dialog box 'Open With' a program?

After I made the Upgrade from Windows Vista premium to Windows 7. These happens when my laptop was attacked by Trojan (rogue/Fake re an). The Firewall was infected and I can't get out. My anti virus was impotent. to quickly resolve the situation I run my Windows 7 and installed the software. Then turn on the Firewall and blocked all Inbound. Then run the MS security scan. After the installation for almost 4 hours. Most of the Program Icons do not launch instead Prompt me with ' Open With ' recommends a program. Thanks Guys.