Recent developments in molecular biology and genetic analysis have inspired strong interests in miniaturization of DNA analysis on a single microfluidic chip. In the last few years there has been tremendous interest in developing a complete biochemical intelligent microsystem for extraction, concentration, amplification, analysis, and processing of DNA. Current biochips are being developed in a very conventional experimental trial and error manner with little computational design support. This paper presents a new software tool, CFD-ACE+, which has been developed for multidisciplinary, multiscale design of biochips. The paper describes the computational physics involved in modeling bio-microfluidic devices, and demonstrates it on a biochip for extraction, concentration of DNA from fluidic samples and on PCR amplification. Other bioprocessing steps such as hybridization and electrophoretic separation in microfluidic networks on a chip, can also be analyzed with CFD-ACE+.