The fuel cell is a very promising power generation system combining the benefits of extremely low emissions, high efficiency, ease of maintenance and durability. In order to promote the commercialization of fuel cells, a flexible forming process, in which a hyper-elastic rubber is adopted as a medium to transmit forming pressure, is suggested as an efficient and cost effective manufacturing method for fuel cell bipolar plates. In this study, the ability of this flexible forming process to produce the micro channel arrays on metallic bipolar plates was first demonstrated experimentally. Then, a finite element (FE) model was built and validated through comparisons between simulated and experimental results. The effects of key process parameters on the forming performance such as applied load and punch velocity were investigated. As a result, appropriate process parameter values allowing high dimensional accuracy without failure were suggested.