Computer aided design (CAD) and simulation tools are key to designing and manufacturing MEMS with higher performance/reliability, reduced costs, shorter development cycles and improved time-to-market. This paper describes a modeling and simulation tool that solves the governing equations for multi-disciplinary physical processes occurring in MEMS. Each physical model is implemented in a module, but all the modules exchange information in a semi-implicit way to achieve fast solution convergence. The fluid model is a pressure-based, implicit 3-D Navier-Stokes solver with capabilities for multi-component diffusion, multi-species transport, multi-step gas phase and surface chemical reactions, and multi-media conjugate heat transfer. The electric model uses both finite volume method (FVM) and boundary element method (BEM) for solving a Poisson’s equation for electric potential. The magnetic model solves for the vector magnetic potential from Maxwell’s equations including eddy currents but neglecting displacement currents. The mechanical model is a finite element stress/deformation solver that has been coupled to the flow, heat, electric, and magnetic calculations to study flow, thermal, electric, and magnetic induced deformations of structures. The electrokinetic model solves the governing equations for electrophoresis and electroosmosis. The capabilities of these models are demonstrated for several MEMS components such as a micro-mixer, a cantilever beam, a comb drive, a valve, a pump, and an electrophoretic chip.