Let's start with something simple. In many recording sessions the guitar amplifiers are brought to a level at which most mortals will choose to stay away from. In many cases, recording at these high volumes will also increase the noise floor of the amp to an audible and annoying level. If you encounter this, do not fear. No need to waste time trying to minimize the noise, especially if the guitar tone is already amazing.
Before you decide to record the noisy amp, go ahead and add another track next to the one assigned to the guitar. You will want to select the same input as that assigned to the guitar as well. Just lower the guitar's volume and record only the noise for the entire length of the track. You should end up with nothing more than a recording of noise.
Bring the noise track to the unity (0) position on the track's fader so that the noise can clearly be heard. Now add a plug-in EQ or any plug-in which features a phase inversion switch. Engage the phase switch.
Reactivate the guitar track you originally intended to record and play it along with the "noise" track. You should now be able to hear only the guitar, as the noise has been canceled out or phase aligned.
After you have completed the guitar recording you will want to add it without the unwanted noise. You will need to bounce or "print" the track with only the guitar and noise tracks soloed.
In ProTools I would simply highlight the length of the track and instantiate the "Bounce To Disc" feature. I would select the sample rate (44.1) and bit depth (24) of the original session, as I will be reimporting it back into the session minus the noise. Choose "Mono Summed" as the file type.
Once the track has successfully bounced, choose Import Audio and select the track. Add it to the Regions List and select New Track, then import to the highlighted "Selection" when prompted.