I record a lot of high gain guitars, and that means that any noise in my signal gets amplified significantly. Unfortunately, my computer emits a 1 KHz tone whenever USB devices are in use - and that includes my Focusrite Scarlett audio interface. That signal gets picked up by my guitar pickups and recorded into Sonar, making the track unusable without a sharp notch filter at 1 KHz.
 
Does anybody have any suggestions on how I can prevent or improve this situation? At the moment, it's looking like "move the computer away from the guitar" is possibly the only practical approach.

Are the USB ports you are plugging into connected directly to the motherboard or are they on a PCI card?   Whatever, the answer, you might try the other approach (USB cards are fairly cheap ~ $10.)

Directly onto the motherboard, currently. I'll look into getting hold of a PCI USB card but it could take a while.

I get this problem in our audio test lab. We resorted to getting isolated USB boxes. I hope you find another way. Plugging everything (PC, sound card, amps, etc) into the same power strip helps a lot, too. Sometimes we just run the laptop off of batteries and that fixes it as well.

What do you mean by isolated USB boxes? The EMI comes from the PC, not the interface itself (at least if waving my guitar around to establish the source is a good guide).
 
Everything's already in the same power strip, just to rule that out. People talk a lot about ground loops but I've not seen any evidence that they are anything other than 50/60Hz. This is clearly an emission from the computer related to USB activity.

Maybe a powered USB hub?  Relatively cheap option to try.

If the guitar is close to the PC... it's going to be hard to completely eliminate EMI type noise (especially if you're using single-coil pickups).
 
You could build a Faraday Cage (copper shielded box) to place over the PC.
This would contain the EMI
 
Some pickups are not well shielded.
I shielded the single-coil pickups in a Jazz Bass (using copper foil)... and that made a huge difference.
As long as the EMI source wasn't directly in front of the single-coils... the noise was greatly reduced (almost eliminated).
 
Poor quality USB cables can also cause "digital hash" type noise.
I encountered this once with a MOTIF ES7.  Swapped the USB cable... and the digital hash noise was gone.

There's some information/ideas in this thread which might be of some help:
 
http://forumsarchive.presonus.com/posts/list/38886.page
 
What quality & length of USB cable are you using?  How close are you to the computer/interface?
 
Sitting further away will help somewhat if feasible.  If you can rotate your sitting position (regardless of how far away you are), you are likely to find a direction which will minimise, if not completely eradicate, the noise.
 
Anyway, looks like a few people found a solution in the above thread, so hopefully it'll be of use to you too.
 
 

I think the issue on the Presonus forum was subtly different - it's the same signal, but theirs is within the system and coming out of the speakers. With my case, it's radiating from the PC and being collected by my guitar.
 
I don't think cables are an issue - the noise comes from the PC rather than the cable. I've tried with the cable from my old printer, but usually I use the cable that came with the interface with the ferrite core on the end - no difference either way.
 
Regarding the other questions - I'm usually about 2 or 3ft from the PC. I can get about 6 or 7ft from the PC at best, but the noise is still too loud, and that makes it a lot less practical to do short takes anyway. Different orientations help but not enough.
 
My guitar pickups are theoretically already well-shielded (EMG 81s and 60s) but obviously they are also just big magnets at the end of the day, and there's only so much the shielding can do.

Jim Roseberry
If the guitar is close to the PC... it's going to be hard to completely eliminate EMI type noise (especially if you're using single-coil pickups).
 
You could build a Faraday Cage (copper shielded box) to place over the PC.
This would contain the EMI
 
Some pickups are not well shielded.
I shielded the single-coil pickups in a Jazz Bass (using copper foil)... and that made a huge difference.
As long as the EMI source wasn't directly in front of the single-coils... the noise was greatly reduced (almost eliminated).
 
Poor quality USB cables can also cause "digital hash" type noise.
I encountered this once with a MOTIF ES7.  Swapped the USB cable... and the digital hash noise was gone.

I've had noise using USB on all of my Yamaha keyboards.  I never leave USB plugged in for them - if I need to record MIDI from them, I'll use a MIDI cable instead.  changing USB cables have never helped, nor has changing anything else.  I've seen on the Motifator forums that this is a fairly typical problem with yamaha USB.