Open your hood. At the back of the engine, you'll see a plastic grating. This is the ventilation intake. Get some Lysol (kills the bacteria) in the scent of your choice and spray it in there. I would 1) turn OFF recirulation, 2) get the fan going on high using the middle vents (not defrost or feet), and 3) spray the lysol for 20 seconds. It'll smell fine after the lysol gets to work.

After this is done, turn off your A/C 30-60 seconds before you stop in order to dry out the system a little.