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 micro wells having a sensing gate bottom and a number of stacked well portions. A bottom surface area of a well portion is different from a top surface area of a well portion directly below. The micro wells are formed by multiple etching operations through different materials, including a sacrificial plug, to expose the sensing gate without plasma induced damage.