To really deep clean a humidifier you should pour a cup or two of vinegar into the humidifier tank and then fill it with water.
Take the humidifier outside and plug the humidifier in and let the humidifier run until the tank of vinegar and water is empty.
The vinegar will help to clean the humidifier out.
You can also just pour some undiluted vinegar into the base of the humidifier and let it sit for 30 to 60 minutes and then use a toothbrush or other soft bristle brush to gently scrub the residue and deposits off.