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Micro-electro-mechanical systems (MEMS) are found in area applications such as the automotive industry, the aviation industry, the semiconductor industry, the medical field, and various other fields where miniaturization is taking over. The accurate measurement of features on the surface of MEMS is an important tool for the assessment and monitoring of product quality. Presented here are the algorithms and results of 3D model reconstructions of MEMS devices using a variety of microscopic sensors. These sensors include an atomic force microscope, a scanning electron microscope, and a laser scanning confocal microscope. MEMS devices with micron-size features were first scanned with these microscopes. 3D models were then built and visualized using methods specific to each microscope. This allows for the models use in applications such as inspection, study of wear and tear, behavior, and reaction of such systems to pressure, heat, and friction.