A method for preparing a semiconductor substrate surface (28) for semiconductor device fabrication, includes providing a semiconductor substrate (20) having a pure Ge surface layer (28) or a Ge-containing surface layer (12), such as SiGe. The semiconductor substrate (20) is cleaned using a first oxygen plasma process (14) to remove foreign matter (30) from the surface (28) of the substrate (20). The substrate surface (28) is next immersed in a hydrochloric acid solution (16) to remove additional foreign matter (30) from the surface (28) of the substrate (20). The immersion step is followed by a second oxygen plasma etch process (18), passivate the surface with a passivation layer (34), and provide for an atomically smooth surface for subsequent epitaxial or gate dielectric growth.