A method for making a MEMS device comprises forming a plurality of micromechanical elements on a first substrate; forming circuitry and electrodes on a second substrate, the first and second substrates extending in a plane in X and Y directions; aligning the first and second substrates in the X and Y directions and moving the substrates toward each other in a Z direction and bonding the first and second substrates with a gap therebetween in the Z direction to form an assembly; singulating the assembly into assembly portions; and altering the gap for each assembly portion. Another embodiment involves aligning the first and second substrates in the X and Y directions and moving the substrates toward each other in a Z direction and bonding the first and second substrates with a gap therebetween in the Z direction to form an assembly; actuating and testing the micromechanical elements of the assembly; and altering the gap for each assembly. A further embodiment involves aligning the first and second substrates in the X and Y directions and moving the substrates toward each other in a Z direction and bonding the first and second substrates with a gap therebetween in the Z direction to form an assembly; wherein the micromechanical elements are actuated while bonding of the substrates.