In this study we describe a novel system for measuring the distribution of inhomogeneous mechanical properties of microelectromechanical system (MEMS) devices. Such inhomogeneous properties are important because they can decrease the reliability of MEMS devices. Our technique involves measuring the variation in the relative position and angle between single molecule markers sprayed on a MEMS device, which indicates the amount of local deformation. The distribution of the deformation on the surface of a MEMS device is calculated from local displacements measured using the system. To simultaneously measure the three-dimensional (3D) position and orientation of the markers, we developed a 3D orientation measurement system that consists of an epifluorescence microscope and a polarization mode converter (PMC). We also detected the 3D displacement and orientation of the torsion bar in a MEMS mirror device.