An optical non-contact measurement system for micro-scale 3D profiles is developed and analyzed in this research. The core concept of the system is based on Shape-from-Focus method. The methodology and the process of the measurement will be explained in this paper. Briefly, corresponding digital images were taken at different heights with predefined step intervals. The properties of images were enhanced by image processing techniques including discrete Gaussian filtering, histogram equalization and high-boost filtering. Finally, the degree of the focused image was quantified by using Sum-Modified-Laplacian algorithm. The height of each pixel was determined with Gaussian Interpolation. 3D geometry model of the specimens can be reconstructed. This system was verified that it can work on the specimen manufactured by laser beam. Analysis of precision will be revealed and the comparison with other measurement methods will be discussed later.