why is system restore ,search,run and formating not working?

my son used a pen drive on a other pc to down load music when he put the pen in my pc and opened it after a avg scan showed no viruses he moved the music to my pc he came across a file he did not know he opend it and it showed my documents thats on my pc and since then my system restore is not working ,the search and run is not on the start menu and i can not format anything . what caused this and how can i fix this ? please help me