Here are our top cleaning tips to avoid mold, biofilm, and bacteria buildup in your trusty humidifier. It’s also important to clean both the water tank and the base of the unit, which houses the fan and motor. Step-by-Step Guide to Humidifier CleaningRemove and empty the humidifier’s water tank. Before draining the diluted vinegar from the base unit, use a small, soft-bristle brush to scrub away all caked-on mold and dirt. Then, pour out the vinegar and rinse the base with clean water.