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Fabrication of the stationary phase for microchip chromatography is most often done by packing of the individual separation channel after fabrication of the microfluidic chip, which is a very time-consuming and costly process (Kutter. J Chromatogr A 1221:72-82, 2012). Here, we describe in detail the fabrication and operation protocols for devices with microfabricated carbon nanotube stationary phases for reverse-phase chromatography. In this protocol, the lithographically defined stationary phase is fabricated in the channel before bonding of a lid, thereby circumventing the difficult packaging procedures used in more conventional protocols.