I was playing in a small MTT today on merge and was doing very well, I felt like I was the dominant player in the field. I was making great decisions and feeling very confident. When it went to 3 handed though all of a sudden I just got ran over and I didn't know how to respond. The guy to my right was a total nit and didn't play a single hand while it was 3 handed. The guy to my left just kept raising me though. I had hands I wanted to take to showdown like Ace high but he made it too expensive by making all of these half pot raises. He had twice as many chips as I had as well. I was dealt a lot of good starting hands for 3 handed but they kept missing and this guy just kept firing half pot bets. His AF was inf when I busted out after I hit a pair of 9s with a flush draw on the flop and he turned a straight with 34o.

So what is the best way to handle this type of player. Tighten up your starting range? Even when I 3 bet he minraised me again, so 3 betting didn't seem to do anything to disuade him from running over me.

post the hands, your question is too general.

3 handed, just play against him when you have position, and play your bb against the nit, fold your small blinds or 3b value hands from it, or bluffs hands (k4s, 89s etc that are easy to get away from but can flop well) but no weak aces/kings small pocket pairs etc.
don't be reluctant to call his 3b in position and to float him when he cbets. he'll often shut down on the turn and you can fire a bet and get him to fold a lot.

but for the most, post the hands

Here is an example of what was happening on almost every hand.

b/c flop isn't good and if he never folds b/f isn't good either, c/f or b/3b.
Did you ever see what he got to showdown with when he minraised in spots like this?
Was he the type of player that would usually call with a T or 7 on this flop?

The only thing I got to see him show down was the 43o that he called from the small blind when I was on the button and he got a straight and I had middle pair but failed to connect on my redraw to the flush. I've never seen anyone that had played 55/35/inf before but it was apparently working for him cause he had a pretty good chip lead. The only other hand I saw him showdown was when he went all in with aces when it was still 7 handed. He didn't get involved with me at all until it became 3 handed, mostly because we were on opposite sides of the table.

I think you have some good advice there with adjusting to a c/f or b/3b line, I guess I need to learn to temper back the agression against agro players. It hurts me sometimes in cash games too.

Cbetting is absolutely fine. Not sure what you're thinking by calling his minraise.