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 device includes a plurality of microwells having a bio-sensing layer and a number of stacked well portions over a multi-layer interconnect (MLI). A bottom surface area of a well portion is different from a top surface area of a well portion directly below. The microwells are formed by removing a top metal plate on a topmost level of the MLI.