Actually, there is software you can use to cool it down. You can use rivatuner to underclock it.
I'll need more details though to really help you out. Is this a custom machine or a consumer machine? Also, if it is a custom machine, explain the cooling system (you'll want to make sure your fans aren't fighting each other). What graphics card (make/model) do you have?
The most likely course of action is to realign your fans if they are misaligned. Replace the heatsing/fan of the gpu... or if it's not worth it... to replace the card and add more cooling fans. Or alternatively, replacing the case.