A novel model based 3D depth measurement technology for micro parts is introduced in this paper. Unlike chemically released parts and assembled integrity by MEMS technology, micro assembly is still a daunting task due to difficulties in parts visualization and assembly autonomy. Conformal mapping has gained popularity due to its usefulness for depth measure in micro parts of the size of human hairs. The processing time to obtain 10 to 100 photos for each pixel and expensive device value, though, hinder commercialization for various micro application industries. In this research, we investigate a novel model based 3D depth measurement technology for faster and cost effective means to promote micro assembly technology in various application fields. Micro parts, by its nature, are known of its shape in advance for the majority of micro applications. We take advantage of the previously known shape of micro parts and hence apply model based approach for a faster and cost effective 3D depth measure. The proposed 3D depth measuring method is based on pattern recognition and multi-focus technique enabling it to extract only information useful for micro parts assembly such as location, size, and height of a micro part. For demonstration purpose, micro gears are fabricated by bulk micro machining technology. In addition, a functioning micro assembly system is developed and used to prove the usefulness of the proposed 3D depth measurement technology.