Embodiments of the present disclosure relate to methods for pretreatment of substrates and group III-nitride layers for manufacturing devices such as light emitting diodes (LEDs), laser diodes (LDs) or power electronic devices. One embodiment of the present disclosure provides a method including providing one or more substrates having an aluminum containing surface in a processing chamber and exposing a surface of each of the one or more substrates having an aluminum containing surface to a pretreatment gas mixture to form a pretreated surface. The pretreatment gas mixture includes ammonia (NH3), an aluminum halide gas (e.g., AlCl3, AlCl) and an etchant containing gas that includes a halogen gas (e.g., Cl2) or hydrogen halide gas (e.g., HCl).