A method and system for preparing a semiconductor wafer are disclosed. In a first aspect, the method comprises providing a passivation layer over a patterned top metal on the semiconductor wafer, etching the passivation layer to open a bond pad in the semiconductor wafer using a first mask, depositing a protection layer on the semiconductor wafer, patterning the protective layer using a second mask, and etching the passivation layer to open other electrodes in the semiconductor wafer using a third mask. The system comprises a MEMS device that further comprises a first substrate and a second substrate bonded to the first substrate, wherein the second substrate is prepared by the aforementioned steps of the method.