In this report, we introduce a surface modification method for the fabrication of discontinuous surface patterns within microfluidic systems. The method is based on chemical vapor deposition (CVD) of a photodefinable coating, poly(4-benzoyl-p-xylylene-co-p-xylylene), onto the luminal surface of a microfluidic device followed by a photopatterning step to initiate spatially controlled surface binding. During photopatterning, light-reactive groups of the CVD polymer spontaneously react with molecules adjunct to the surface, such as poly(ethylene oxide). We demonstrate the potential of these reactive polymers for surface modification by preventing nonspecific protein adsorption on different substrates including silicon and poly(dimethylsiloxane) as measured by fluorescence microscopy. More importantly, three-dimensional patterns have successfully been created within polymer-based microfluidic channels, establishing spatially controlled, bioinert surfaces. The herein reported surface modification method addresses a critical challenge with respect to surface engineering of microfluidic devices, namely, the fabrication of discontinuous patterns within microchannels.