The emergence of disposable low-cost microfluidic devices for various medical diagnostic tests brings with it a need for high volume high quality production methods for this micro-scale product. This paper reports on the development of a manufacturing cell for a polymer microfluidic device produced by hot micro-embossing and tape closure. The cell includes highly instrumented, and uses novel embossing and in-process metrology equipment. Its use is demonstrated in a series of statistical process control experiments, and followed by an automated experiment designed to identify an optimal operating point for the process to account for part accuracy, variability and production time.