In order to realize the three-dimensional measurement of micro electro-mechanical systems (MEMS), it is usually necessary to use a microscope or an optical profilometer. However, the traditional method has problems such as low precision and high cost of detection equipment, and it cannot achieve good results for an MEMS structure with many fracture surfaces. A new method for 3D measurement and image processing was presented in this paper. Unlike the three-dimensional reconstruction measurement method of multi-angle microscopes, this study firstly used a monocular microscope to obtain a series of single point measurements of the target, thus acquiring the depth information through single axial images. Then, a defogging algorithm was adopted for image preprocessing, denoising, and achieving effective information extraction. Subsequently, the depth information of the object to be tested was obtained using a focus measure algorithm. Finally, 3D fitting was performed using the data processing software. Based on the above principle, the focal plane array (FPA) was taken as the target to be measured. The experimental results show that the proposed 3D reconstruction method and image processing algorithm can obtain a more accurate FPA morphology, and can clearly show the release hole reflecting surface and the leg part on the reflector. The leg length of the FPA is measured to be 110.6 μm, and the pixel size of each reflector is about 120.8 μm×70.8 μm, which is consistent with the design value. It solves the problem of measuring the fracture surface, and reduces the difficulty and cost of microstructure measurement. The multi-directional image-fusion measurement technology using a monocular microscope is of great significance for MEMS 3D profile measurement. The defogging algorithm has significant application value in image fusion and 3D measurement image processing.