The present disclosure provides a biological field effect transistor (BioFET) and a method of fabricating a BioFET device. The method includes forming a BioFET using one or more process steps compatible with or typical to a complementary metal-oxide-semiconductor (CMOS) process. The BioFET includes a microwells having a sensing layer, a top metal stack under the sensing layer, and a multi-layer interconnect (MLI) under the top metal stack. The top metal stack includes a top metal and a protective layer over and peripherally surrounding the top metal.