The present invention provides a MEMS structure comprising confined sacrificial oxide layer and a bonded Si layer. Polysilicon stack is used to fill aligned oxide openings and MEMS vias on the sacrificial layer and the bonded Si layer respectively. To increase the design flexibility, some conductive polysilicon layer can be further deployed underneath the bonded Si layer to form the functional sensing electrodes or wiring interconnects. The MEMS structure can be further bonded to a metallic layer on top of the Si layer and the polysilicon stack.