In order for analysis of DNA to become available for routine clinical use, low cost methods of manufacturing instruments need to be developed. One approach is to take advantage of the microfabrication to reduce the overall size of different instruments, reduce the volume of expensive reagents required for analysis, and increase throughput. A suite of modular micro-instruments is being developed for the improved detection of colorectal cancer. Modules are being designed to be molded for efficient production and to stack together interchangeably for flexible use. Individual modules for the polymerase chain reaction (PCR) for DNA amplification, ligase detection reaction (LDR) for rare mutation identifcation, and both capillary elecrophoresis and zip-code array detection have been demonstrated. Mathematical models of the key performance characteristics of the each chip were used to guide design. Mold inserts have been fabricated using either LIGA (Lithography, Electrodeposition, Molding) or UV-LIGA and supplemental micro-milling or laser machining. The mold inserts were used for hot embossing polycarbonate or PMMA replicas of the devices. The continuous flow PCR performance was compared to conventional instruments and a study of the effect of flow velocity on the biochemical output of the device was performed. Robust, high speed amplification was demonstrated for different length fragments.