Didn't say which brakes you have, so hard to tell what is causing the noise and what steps you could take to improve. Could be cheap or mismatched rotors, could be contaminated pads. The rotors probably needs to be trued, which you can do with a special tool (Park makes one) or a large adjustable wrench. The truing tool bends the rotor closer to the center of the rotor, which works better. The calipers may need to be centered and adjusted.
I have SLX hydraulic disc brakes, use recommended rotors, and have perfectly trued the rotors, so no squealing and no scraping. If the pads are wet in the rain, fog or after rinsing the bike, they will squeal a little until they dry out after a few rotations.