A method and apparatus for removing excess dopant from a doped substrate is provided. In one embodiment, a substrate is doped by surfaced deposition of dopant followed by formation of a capping layer and thermal diffusion drive-in. A reactive etchant mixture is provided to the process chamber, with optional plasma, to etch away the capping layer and form volatile compounds by reacting with excess dopant. In another embodiment, a substrate is doped by energetic implantation of dopant. A reactive gas mixture is provided to the process chamber, with optional plasma, to remove excess dopant adsorbed on the surface and high-concentration dopant near the surface by reacting with the dopant to form volatile compounds. The reactive gas mixture may be provided during thermal treatment, or it may be provided before or after at temperatures different from the thermal treatment temperature. The volatile compounds are removed. Substrates so treated do not form toxic compounds when stored or transported outside process equipment.