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Purchase a mold and mildew fighting disinfectant aerosol spray, such as a specialty duct cleaner. Alternatively, make your own all-natural spray with a vinegar and water. Turn the car, fan, and the AC all the way off. Spray your disinfectant into every single vent. Turn the car on and the AC to max power, full blasting fan. Find your re-circulation vent and spray into it generously, with the AC still running. Switch the AC from "max" to full fan mode. For serious issues, lift the hood, replace the cabin air filter and spray down all the intake lines. Run the car, doors open, with the AC off and the fans on full for five minutes. Take the car to your dealer if the smell persists.
Specialty sprays may be the best bet for serious odors, but for smaller problems (or to stay ahead of potential smells) you can use an over-the-counter disinfectant spray like Lysol. Mix up one part white vinegar with three parts water, then put it in an old spray bottle or solvent sprayer. While vinegar isn't the most pleasant smell, it will fight the mildew naturally and it will fade off quickly. Throw in the juice from half a lemon to get a slightly fresher and longer lasting scent. Flick both switches into the off position and make sure the car isn't running. Make sure you get in the backseats and hit the vents at your feet, which often pump the most air. There are also vents on the dashboard, and usually one on the pointing on the back windshield as well. Keep the doors closed as you do this. You want the cleaning fluid to get in the system. This will start to circulate air around the system for you, getting your cleaning solution around the AC system. Keep it on this "Max" setting at first to kick the system into gear. You can find your re-circulation vent by checking your manual. It is often on the drivers side floor, near the console, or in the trunk. The little button with arrows pointing a circle tells your car to stop taking air from the outside, and instead recycle the air from the inside. Press this button if you have it, then spray down this vent to make sure your cleaning fluid is staying in the system. You want to be blowing more air, not cooling more air. This should prevent additional moisture from coming in. If you have nasty odors coming from the car and no way to stop them, grab your owner's manual and lift the hood. The AC system is back towards the windshield, under the plastic grate and filter where  (different models have different methods -- you must check your manual), and remove the filter, cleaning and replacing when necessary. While there, spray the whole apparatus down with your cleaning aerosol to fight and kill any mold or mildew. This is your final "drying out," and it will prevent mold and mildew from reestablishing your old odors. If the smell still won't go away, don't ignore it. It won't get any better on its own. Take it to the dealer to make sure the smell is not the cause of something more serious, and to handle the problem before it becomes worse than just a bad smell.