Well, you could have a real problem depending on how enterprising the little guy was. I can't see how the critter could get past the A/C evaporator if he entered your hvac system from the air inlet. It pretty well seals off the interior ducting from the evap case. But if he got in from the inside of the car through the heater or a/c ducting, you may have to bite the bullet and pull the dash and separate the plenum to get it all.
First thing to check...pull the fan motor from under the hood. That's where 99% of these type of problems end up. And it's probably the reason you are hearing noise as the fan is hitting the nest. You should be able to clean all of it from there. Do this quickly in case you killed some critters and they start to stink.