Due to the broad impact of microfabrication technology on chemistry and biology, new methods to pattern and etch a variety of materials are being explored in a number of laboratories. Here, we report the design, fabrication, and operation of a glassy carbon (GC) microchip interfaced to a nanoelectrospray ionization source and a quadrupole mass spectrometer. The method involves standard photolithographic pattern transfer to a photoresist layer and anodization of the exposed GC substrate in basic electrolyte to produce a series of channels with well-defined wall structure. The performance of the microchip was evaluated with standard polymer and peptide samples.