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 to form an etched surface of the silicon-containing substrate and forming an epitaxial layer on the etched surface of the silicon-containing substrate. The plasma etch process comprises flowing an etchant gas mixture comprising a fluorine-containing precursor and a hydrogen-containing precursor into a substrate-processing region of a first processing chamber and forming a plasma from the etchant gas mixture flowed into the substrate-processing region.