Embodiments of the present invention generally relate to methods for removing contaminants and native oxides from substrate surfaces. The methods generally include exposing a substrate having an oxide layer thereon to an oxidizing source. The oxidizing source oxidizes an upper portion of the substrate beneath the oxide layer to form an oxide layer having an increased thickness. The oxide layer with the increased thickness is then removed to expose a clean surface of the substrate. The removal of the oxide layer generally includes removal of contaminants present in and on the oxide layer, especially those contaminants present at the interface of the oxide layer and the substrate. An epitaxial layer may then be formed on the clean surface of the substrate.