Wow, I haven't heard anybody even talk about this as a problem in like... 12 years, maybe? How are you even managing to capture the sound of a modern CPU in a guitar performance? I can't even think of a more specific question, lol. How are you recording this? Are you using a 1/4" to 1/8" adapter and running your guitar into an onboard microphone input? That's the only way I can even see it being maybe an issue...
You sure you're not just hearing noise from a crappy soundcard? Or a groundloop?