Out of several critical issues, particles as well as bonded surface contamination are matters of great concerns, when considering wafer bonding in MEMS and Semiconductor fabrication technology. This study aims at reporting the development of a bonded wafer inspection system, by analyzing transmittance deviations and the changes of the intensity caused by the defect thickness.In this method, laser beam transmission is utilized to detect the exact location of defect in bonded wafer.To this end, optical design software is used while Monte-Carlo (MC) simulation approach was applied. Accordingly four parameters are considered to have more influences on irradiance distribution (uniformity) and defect detection accuracy in the system, namely; distance between each adjacent laser source, distance between laser source and diffuser, distance between diffuser and SOI wafer, and diffuser type.Using design of experiments, all produced data from screening were analyzed and optimized solution for the best irradiance distribution and detection accuracy was achieved. Implementation of the system has been done by comparing DOE optimized result with experiment result and ensuring the detection accuracy.