Yes and no. Per the manual;
PROFILING with Effects in the Recording Chain
Many guitarists get their signature sound by combining their tube amp with distortion pedals, booster pedals, and equalizers/filters. If you want to, you can keep these in the signal chain during the PROFILING process - they will all be accurately included as a part of the reference amp sound. However, there are a few exceptions: some distortion pedals use a special design that cannot be captured accurately, for instance the Tube ScreamerTM.
If you do include your effects chain with your Amp PROFILE, but are not happy with the result, try again without the distortion pedal. Remember, you can always use one of the modeled distortion pedals in the PROFILER instead, when building your Rig.
Other effects should be bypassed during the PROFILING process because they will adversely affect the result, making it sound less natural, and different to the original amp tone. These include compressors, noise gates, and time/modulation/reverb effects such as delay, reverb, chorus, and so on.
You might also run into trouble when PROFILING a sound in which both the pre- and power amps of the reference amplifier are driven into distortion. If the resulting PROFILE sounds unsatisfying, try to reduce the volume of the power amp. This will make the sound somewhat more transparent, without significantly reducing the amount of distortion. The same is true for those modeling amps which offer a separate gain control for pre- and power amp.
The PROFILER only allows for mono PROFILING. Stereo PROFILING is not currently supported, but really, how many classic guitar amps feature true stereo circuitry, anyway?
Since the PROFILER sends its own test-tones into the reference amp during PROFILING, it should be obvious that the sound of your guitar isn’t part of the result. The PROFILER is designed to react to any guitar in an identical way to the reference amp.