Using both wet and plasma etching, we have fabricated micro-channels in silicon substrates suitable for use as gas chromatography (GC) columns, Micro-channel dimensions range from 10 to 80 mu m wide, 200 to 400 mu m deep, and 10 cm to 100 cm long. Micro-channels 100 cm long take up as little as 1 cm(2) on the substrate when fabricated with a high aspect ratio silicon etch (HARSE) process. Channels are sealed by anodically bonding Pyrex lids to the Si substrates. We have studied micro-channel flow characteristics to establish model parameters for system optimization. We have also coated these micro-channels with stationary phases and demonstrated GC separations. We believe separation performance can be improved by increasing stationary phase coating uniformity through micro-channel surface treatment prior to stationary phase deposition. To this end, we have developed microfabrication techniques to etch through silicon wafers using the HARSE process. Etching completely through the Si substrate facilitates the treatment and characterization of the micro-channel sidewalls, which dominate the GC physico-chemical interaction. With this approach, we separately treat the Pyrex lid surfaces that form the top and bottom surfaces of the GC flow channel.