How can I open a program which will not let me on my computer?

I got some kind of trojan or something on my computer. 2011 antirvirus or something. I did a scan in safe mode as administrator because it wont let me as normal account user. But I do not think it deleted the trojan. I tried to scan in normal mode but the program wont open. No programs will open. not even Firefox. When I try to open a program....I get a popup now saying OPEN WITH..............CHOOSE THE PROGRAM YOU WANT TO USE TO OPEN THIS FILE. Also when I try to run MSCONFIG I get same popup..asking which program to use to open MSCONFIG..that is crazy. Can someone please help?