Micro-opto electromechanical systems are of growing importance in the development of new miniaturised projection, imaging and detection technologies. Because of the increasing complexity of construction involving layers of microelectronics, optoelectronics and micro-optics, di erent types of defects can appear that need to be understood and controlled in order for the miniaturised system to operate correctly within the given speci cations. We have recently developed a miniaturised structured light (micro-opto electromechanical systems) projector consisting of a multilayer sandwich made of a rst layer of 3 bars of 12 VCSEL laser sources, a second layer of Fresnel collimating lenses (di ractive optical elements) and a third layer of Fourier di ractive optical elements to produce the structured light pattern. The main defects that had to be controlled were alignment errors, the rst ones being between the emitting surface and the collimating lenses and the second one concerning the lateral alignment of the photomasks used to produce the 4 levels of the Fourier elements. We demonstrate how 3D geometrical shape characterization of the emitting structures and di ractive optical elements surface structures using coherence scanning interferometry played a major role in the conception and fabrication of a prototype micro-optoelectromechanical projection system to understand the source of the alignment errors and to minimise them.