Punch recording

Is there a way to minimize the audible "click" that occurs when using a punch in to change a few notes? I can get the right inflection, tone etc. from the guitar but there always seems to be an abruptness at each end of the punch that is audible from that point on. Tried the crossfade as that seemed it would be the solution but it just seems to make it worse, unless i am not using that feature correctly.