Portable electronic devices such as notebook computers, PDAs, cellular phones, etc., are being widely used, and they increasingly need cheap, efficient, and lightweight power sources. Fuel cells have been proposed as possible power sources to address issues that involve energy production and the environment. In particular, a small type of fuel-cell system is known to be suitable for portable electronic devices. The development of micro fuel cell systems can be achieved by the application of microchannel technology. In this study, the conventional method of chemical etching and the mechanical machining method of micro end milling were used for the microfabrication of microchannel for fuel cell separators. The two methods were compared in terms of their performance in the fabrication with regards to dimensional errors, flatness, straightness, and surface roughness. Following microchannel fabrication, the powder blasting technique is introduced to improve the coating performance of the catalyst on the surface of the microchannel. Experimental results show that end milling can remarkably increase the fabrication performance and that surface treatment by powder blasting can improve the performance of catalyst coating.