A method for achieving greater uniformity and control in vapor phase etching of silicon, silicon oxide layers and related materials associated with wafers used for semiconductor devices comprises the steps of first cleaning the wafer surface to remove organics, followed by vapor phase etching. An integrated apparatus for cleaning organic and, subsequently, vapor phase etching, is also described. In embodiments of the invention cooling steps are incorporated to increase throughput, an on-demand vaporizer is provided to repeatably supply vapor at other than azeotropic concentration, and a residue-free etch process is provided.