To get completely clean sounds with my stock 54 Stratocaster I have to turn the input gain to at least 0.5 even on clean Fender amps like the Twin Reverb, or Deluxe Reverb set at low volumes. I can not set the Fender amps in the Axe FX like I do for clean sounds on the same amps in real life and get the same clean sound. It is way more touch sensitive than on the real amps. On the real amps I can set the amps clean, and if I play harder it just gets louder, it doesn't distort when I play harder like to does with the Axe FXIIXL+ or Axe FXIII. I've literally had to learn to play with a much softer touch than I normally use when playing through real Fender amps if I want a completely clean sound with the Axe FXIII. Or use a compressor, which I don't need to use with the real amps. You can get a great totally clean amp sound though with everything set right.
Check your guitar action. Any fret buzz, nut buzz, or bridge buzz, at all is very noticeable and unforgiving on the Axe FXIII.
I recently had to get the nut filed on a telecaster that was causing a buzz I couldn't figure out where it was coming from.
Two strings were buzzing at the nut.
Turn off the input noise gate completely and try it. I don't use it on clean sounds.
Make sure nothing is clipping in your preset. There are several tutorial videos that stress this and go through this in detail.
Make sure nothing is clipping in your interface or your DAW.
If none of those things work I'd contact support. I can't think of anything else that might be the problem.