Implementations of the present disclosure generally relate to methods and apparatuses for epitaxial deposition on substrate surfaces. More particularly, implementations of the present disclosure generally relate to methods and apparatuses for surface preparation prior to epitaxial deposition. In one implementation, a method of processing a substrate is provided. The method comprises etching a surface of a silicon-containing substrate by use of a plasma etch process, where at least one etching process gas comprising chlorine gas and an inert gas is used during the plasma etch process and forming an epitaxial layer on the surface of the silicon-containing substrate.