Check the air flow direction on the case fans, in most cases it should be air in at the front out at the back. The case fan should have a direction arrow on it. Also make sure that the heat exchanger on the CPU is clean of dust.
It would be an idea to give people a more comprehensive listing of your system specifications, particularly hardware, that will enable some more specific recomendations.
You could also use Everest click here to see what temperatures you are running at.