To clean your car's air conditioning system, firstly address the components responsible for the flow of air from outside to inside the vehicle. Vacuum out and clean the interior air vents, replace the cabin filter and if you have access use compressed air to blow out the air condenser in the engine bay. These steps should reduce the amount of unwanted particles entering the cabin. If you want to go a step further you can buy air conditioning sanitisers from companies such as Autoglym. These work by setting your air conditioner on recirculation mode and release a sanitising spray that then circulates throughout the system.