For well resolved electrokinetic separation, we utilize crystalline quartz to micromachine a uniformly packed separation channel. Packing features are posts 5 micrometers on a side with 3 micrometers spacing and etched 42 micrometers deep. In addition to anisotropic wet etch characteristics for micromachining, quartz properties are compatible with chemical solutions, electrokinetic high voltage operation, and stationary phase film deposition. To seal these channels, we employ a room temperature silicon-oxynitride deposition to form a membrane, that is subsequently coated for mechanical stability. Using this technique, particulate issues and global warp, that make large area wafer bonding methods difficult, are avoided, and a room temperature process, in contrast to high temperature bonding techniques, accommodate preprocessing of metal films for electrical interconnect. After sealing channels, a number of macro- assembly steps are required to attach a micro-optical detection system and fluid interconnects.