A method of cleaning a microwave plasma applicator tube as described herein includes preparing a microwave plasma applicator for cleaning. A general cleaning of the plasma applicator tube is performed using an organic solvent wash and an ultrapure water wash. Selective cleanings of the tube are performed to remove selected contaminants. Such cleanings include a third wash with an alkaline cleaning solution, a fourth wash with an acidic cleaning solution and another wash using an ammonia and peroxide solution. The tube is rinsed using a sonicating wash performed in ultrapure water followed by drying. Also, the coil can be cleaned using acidic wash solution.