When recording piano I've always struggled to get clean punches. I usually try to punch just ahead of a downbeat when the pianist is lifting the sustain pedal, but I often end up with some remnants of the previous chord hanging over, and this sound tends to vary from take to take so that my punch is pretty obvious.
Hopefully my description makes some sense. What should I be doing different?
Assuming you're talking digital:
Punching in can be tricky, since no musician starts at exactly the same point in time on every take. Fingerstyle guitar has similar problems; there are always overtones hanging around.
I dupe the track I want to punch into, but without audio. (I.e., preserving settings, gain, and so on.) Then, record the bit of music in question onto the dupeed, empty track. Last, edit it into the track original. I can always get a much cleaner sound that way.
Edit: If you're capturing the musician's performance via midi, I'd try editing the data so what the left and right hands are playing are on separate tracks, this might give you a little more flexibility when editing.
If you're working in a computer, and you record a second track in addition to the original, you can apply a crossfade or volume envelope after the recording is completed, to fade the portion of the new track you want into and out of the mix, and then you won't have to worry about getting the punch perfect.
If you cannot punch in right as the sustain pedal is released, you'll want to have the pianist listen to what s/he is playing before the punch point and try to match it as closely as possible so that the sustained notes don't sound to weird. Depending on the complexity and length of the piece, it might be better to just to the entire thing over again :(
