A method and apparatus for cleaning layers of solar cell substrates is disclosed. The substrate is exposed to a reactive gas that may comprise neutral radicals comprising nitrogen and fluorine, or that may comprise anhydrous HF and water, alcohol, or a mixture of water and alcohol. The reactive gas may further comprise a carrier gas. The reactive gas etches the solar cell substrate surface, removing oxygen and other impurities. When exposed to the neutral radicals, the substrate grows a thin film containing ammonium hexafluorosilicate, which is subsequently removed by heat treatment.