Stockfish is known to be very processor intensive but it's programmed to make full use of all processor cores.
Are there any options in whatever GUI you're using to reduce the processor priority?
If not you could perhaps try a different GUI and maybe even a different engine as well.
Arena and Tarrasch chess GUI's are both freeware if you're wanting to experiment.
I know Arena definitely has settings to allow you to adjust the processor priority but I'm not sure about Tarrasch. Arena seems more advanced to me in any case so if I were you I'd be inclined to try that one first.
Critter is a highly rated UCI chess engine with an ELO rating very similar to Stockfish and it's available for free. Rybka is also very highly rated and is free up to version 2.3.2a so you may like to try that too.