We developed a system to analyze microscopic deformation, which can visualize inhomogeneous deformation in MEMS(Micro Electro Mechanical Systems) devices by using single-molecule markers. As MEMS devices become smaller, their mechanical properties seem to become inhomogeneous. This causes an undesirable distribution of deformation and stress, and decreases the reliability of the MEMS devices. We distributed fluorescent single molecules discretely on the microstructure of a MEMS device, and traced their relative displacements and rotations by observation under a three-dimensional orientation microscope, which provided information about normal, torsional, and bending displacements.