Will a aftermarket cd player work with the mach 1000 system?

i have a 02 mustang gt with the mach 1000 stereo system it came stock with this car. has 4 amps and 2 10" subs. i recently bought the car from a guy who said his nephew stuck a cd in when there was one in already. my question is if this cd cant be taken out without ruining the cd player can i replace it the mach1000 head unit with an aftermarket cd player and have it still work with the mach1000 subs and speakers. or do i have to replace the whole system?