How can I access my computer programs again?

I was able to use a free anti-malware program to remove a trojan virus (It might still be in the background but so far no problems) however I can't access my computer programs such as AOL or even certain windows applications like system information. I keep getting asked what program I want to use to open these files with yet when I browse onto the correct program files, I'm redirected back to the "open with" window. Have these files been deleted? Will system restore work? (k that doesn't open either so nvm) Do I have to reinstall windows?