You probably have a build up of moisture and bacteria in the evaporator or associated trunking / pipework. As you use the A/C you get condensation build up which is the usual cause of the musty smell and this promotes the bacteria build up. What you need is what's commonly known as an 'aircon bomb' or anti bacterial cleanser.

Most motor factors sell a variation of these. Some come as an aerosol spray that you can lock the nozzle and leave inside the car with the fan blowers on, re circulation on and vents open to distribute the gas throughout the system. Some come as a spray foam type with a long, thin pipe that you insert into the air vents, pollen filter housing and evaporator drain hose etc.

Choose which type is best for you and leave the blowers running for around 10 minutes or more to let the cleanser mist/foam do its thing with all the windows closed. You may then need to continue running the blowers for a few minutes with the windows open to get rid of the smell of the cleanser as some of them can be a bit overpowering.

It's also best to remove the pollen filter and fit the cover whilst you cleanse the system to prevent it getting damp. If it's still good, refit it. If not, fit a new filter.

http://www.ebay.co.uk/itm/WURTH-AIR-CONDITIONING-DISINFECTANT-SPRAY-AIR-CON-CLEANER-300ml-INC-PIPE-/231243138754?pt=LH_DefaultDomain_3&hash=item35d72a46c2

or if you can't get underneath at the drain:

http://www.ebay.co.uk/itm/Comma-Aircon-Cleaner-150ml-Aerosol-/390927892469?pt=LH_DefaultDomain_3&hash=item5b051e3ff5

and can be had from Halfords if you're eBayphobic.