Native oxides and residue are removed from surfaces of a substrate by performing a multiple-stage native oxide cleaning process. In one example, the method for removing native oxides from a substrate includes supplying a first gas mixture including an inert gas onto a surface of a material layer disposed on a substrate into a first processing chamber, wherein the material layer is a III-V group containing layer for a first period of time, supplying a second gas mixture including an inert gas and a hydrogen containing gas onto the surface of the material layer for a second period of time, and supplying a third gas mixture including a hydrogen containing gas to the surface of the material layer while maintaining the substrate at a temperature less than 550 degrees Celsius.