Methods for protecting a cadmium sulfide layer on a substrate are provided. The method can include sputtering a cadmium sulfide layer onto a substrate from a cadmium sulfide target at a sputtering pressure (e.g., about 10 mTorr to about 150 mTorr), and sputtering a cap layer directly on the cadmium sulfide layer. The cap layer can be sputtered directly onto the cadmium sulfide layer without breaking vacuum of the sputtering pressure. Methods are also provided for manufacturing a cadmium telluride based thin film photovoltaic device through depositing a cadmium sulfide layer on a substrate, depositing a cap layer directly on the cadmium sulfide layer, heating the substrate to sublimate at least a portion of the cap layer from the cadmium sulfide layer, and then depositing a cadmium telluride layer on the cadmium sulfide layer. An intermediate substrate for forming a cadmium telluride based thin-film photovoltaic device is also provided.