software

HELP
Hello I am pretty proficient in Computers But I am stumped.
My wife the other night was watching you tube and was downloading an update to her pda/scanner for for her work after she turned the system off.
I awoke to turn the system on and it booted to my desktop then all of a sudden all icons start bar disappeared except for the background picture.
When I was able to launch IE it would give me an error that this is an invalid extension ,also task manager would not come up it says it has been disabled by the admin. I managed to get mozilla up. I ran a virus scan said it found 3 trojans but quarantied them.