In the last few years there has been tremendous interest in developing a complete biomedical/biochemical intelligent microsystem for extraction, concentration, amplification, analysis and processing of DNA. This paper presents multi-disciplinary computational tool, CFD-ACE+MEMS, for simulation and design of microfluidic bioMEMS. It is demonstrated on 3D high-fidelity simulations in microfluidic channels and on a complex DNA filtration chip.