Could be idle control valve, could be a bad vaccum leak also, could be dirty fuel injectors. So here what you do first, spray the degreaser/cleaning stuff into the idle control valve, put some injector cleaner through (can't remember the brand name... something like 40k or 401k or something like that.. any one know the one I am talking about? comes in a can you pour in the fuel tank, or in a direct injection canister thing?) That should take care of it. If not you might need to take the idle control valve out and clean very well, replace O2 sensor, Mass air flow sensor, or vaccum leak could all be other possiblilities.
The other question is are you sure that they replaced the fuel filter correctly and the air flow meter? If that was just replaced and this thing just started, I would double check the installation. Or did this happen a bit afterward?