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Due to MEMS device needs highly accurate design, a novel design methodology for MEMS device is put forward in this paper. Firstly, top-down and bottom-up hybrid design process based on IP library is proposed. It facilitates and speeds up design cycle and reduces the expense of MEMS design by using IP components which have been successfully implemented. Secondly, virtual fabrication process is proposed. It is used to establish stable, accurate and robust 3D geometry of device according to the fabrication process. Voxel-based visualization technique is applied to virtual fabrication process to achieve better process simulation result. It could help designers achieve highly accurate fabrication process and result. Thirdly, virtual operation is proposed. It is used to visualize and simulate the mechanical operation of MEMS device. This module could exhibit 3D realistic animation in virtual reality (VR) environment. It could help designers achieve highly accurate physical operation characteristic of MEMS device. With the help of virtual fabrication process and virtual operation, intuitive image and realistic animation of MEMS device is exhibited at the design stage. An available prototyping MEMS CAD which implements both top-down and bottom-up design notion integrates with virtual fabrication process and virtual operation. A bimetallic thermally-actuated micropump is studied through the paper using this novel design methodology.