A method of fabricating a microelectromechanical system (MEMS) device includes providing a semiconductor substrate having a semiconductor layer and an interconnect structure. A passivation layer and a photoresist layer are formed over the interconnect structure and a plurality of openings are formed in the photoresist layer to expose portions of the passivation layer. The passivation layer exposed by the openings and the interconnect structure thereunder are removed, forming a plurality of first trenches. The semiconductor layer exposed by the first trenches is removed, forming a plurality of second trenches in the semiconductor layer. An upper capping substrate is provided over the passivation layer, forming a first composite substrate. The semiconductor layer in the first composite substrate is thinned and portions of the thinned semiconductor layer are etched to form a third trench, wherein a suspended micromachined structure is formed in a region between the first, second and third trenches.