Can you explain a bit about the situation, the gear, the software, etc.?
Since this is a home recording forum, I assume you're talking about making tracks sound in tune with each other, not about a group of performers who can get in tune before playing-- but if you're recording a performance, then that might apply, too.
As for gear, I'm not talking about your guitar, audio interface, mixer, etc., but rather any MIDI hardware you might be using. For instance, if you've got a MIDI file playing on a keyboard and you're recording the audio output of the keyboard, the keyboard itself (i.e., brand and model) will determine what sort of tuning functions it does or doesn't have, or whether it can or can't respond to any MIDI tuning messages, etc., so it would be helpful to know the hardware you're dealing with.
And as for software, knowing the DAW would be helpful so people having experience with that particular DAW might offer suggestions-- but more to the point, if the MIDI parts are being played by virtual instruments then knowing which virtual instruments you're using would be helpful. For instance, if you're using a particular soft synth then it may have some controls for adjusting the coarse tuning and fine tuning, or settings for adjusting the scale tuning, etc.
As far as general advice and suggestions that could apply to any situation, set of gear, and software, Rob's mention of chorus, delay, and phasing is helpful-- try adding a bit of chorus to the tracks to see if it helps. Otherwise, if you're going for an effects-free sound, listen to the tracks carefully for the spots where things sound out of tune and try to identify the offending part(s) and note(s), then see if you can better tune the guilty instrument or note at the source, or if tuning and re-recording isn't feasible then maybe try a bit of pitch-shifting as needed on the existing tracks.