Methods and apparatus for removing oxide from a surface, the surface comprising at least one of silicon and germanium, are provided. The method and apparatus are particularly suitable for removing native oxide from a metal silicide layer of a contact structure. The method and apparatus advantageously integrate both the etch stop layer etching process and the native oxide removal process in a single chamber, thereby eliminating native oxide growth or other contaminates redeposit during the substrate transfer processes. Furthermore, the method and the apparatus also provides the improved three-step chemical reaction process to efficiently remove native oxide from the metal silicide layer without adversely altering the geometry of the contact structure and the critical dimension of the trenches or vias formed in the contact structure.