Not enough attention has been devoted to developing the manufacturing processes required to transition fuel cell science into commercially viable products, despite clear recognition that cost and reliability are two key factors preventing more rapid introduction of the technology. Understandably, there is a natural reluctance of many companies to invest resources in manufacturing processes and systems for a product that is still evolving. Changes in materials, geometries, and even the basic fuel cell architecture can have profound effects on the viability of certain manufacturing processes and equipment. This situation suggests that modular flexible manufacturing processes be adopted to accommodate these uncertainties. Since 1999 researchers in the Center for Automation Technologies and Systems (CATS) at Rensselaer Polytechnic Institute have focused on developing flexible manufacturing processes and systems for the manufacture of high temperature proton exchange membrane (PEM) fuel cell components. One result has been a fully automated membrane and electrode assembly (MEA) pilot manufacturing line developed for BASF Fuel Cell, GmbH, formerly Pemeas, GmbH that has been operating since September of 2002. This pilot line has been designed as a highly flexible modular manufacturing system that is able to respond quickly and cost effectively to changes in product materials, geometries, and architectures. For example, the line has easily accommodated three generations of membrane materials and a broad range of MEA sizes and geometries. Because of this flexibility, short runs of prototype MEAs are feasible, and the pilot line is able to produce a high mix of a broad range of MEA sizes. The CATS research team continues to optimize manufacturing processes to provide increased capacity, consistency, reduced costs, and high product quality. This paper will describe the many challenges and risks associated with the development and implementation of an advanced manufacturing capability for high temperature PEM MEAs, and the continuing collaboration between the BASF Fuel Cell and the CATS. Specific examples of several technical challenges and the adopted solutions are presented, along with ongoing fuel cell manufacturing initiatives.