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Micro-electro-mechanical system (MEMS) feature coupling of multiple energy domains, integration of multiple discipline, and mixing of analogy and digital signals. Therefore, the design of MEMS must recur to computer aided design (CAD). Aiming at the characteristic and the unique design method of MEMS, a design flow is proposed for MEMS CAD. Meanwhile, a structured layering designed method is constructed, and some key technologies are discussed.