Are you looking for notation or sequencing? A good notation program will let you clean up the music staff, a sequencer will let you edit the MIDI to get it like you want--I use(well, when working, which has been a while) Overture, which allows both, to a degree--but is expensive, and, I've had to invest a lot of time in tracking it from one owner to the next--

My suggestion is to simply listen to the MIDI until you've memorized it, then type it into your notation program yourself--it'll save a lot of editing time--