A method (100) of making a semiconductor device, for example a light emitting diode. The method (100) includes providing (105) a semiconductor wafer, and providing (110) a protective layer over the semiconductor wafer. Preferably the protective layer comprises indium-tin oxide. Processing steps are performed on the wafer and the protective layer is arranged to protect the wafer during the processing steps. The processing steps may include forming a mask layer (115) over the protective layer, which is used for etching through the protective layer and into the semiconductor wafer, removing the mask layer, or etching filling materials (150) provided over the selectively etched semiconductor wafer.