This study represents the efficient depth measurement for 3-dimensional microsystems using the disparity histogram from stereo images. Implementation of user-friendly Windows program written in C++ involves the various methods for the stereo-image processing in which the minimization of matching-pixel error upon the unique point for stereo images was carried out as a pre-processing method. Even though MPC among various methods was adopted in the present measurement, the resulting measurements seem to require optimizations of the windows sizes and corrections of post-manipulation for stereo images. The present work using Windows program is promising to measure the 3-dimensional depth of micro-system efficiently in implementing the 3-dimensional structure of micro-systems.