The fabrication and characterization of chemical patterns using a technique that can be readily integrated with methods currently used for the formation of microarrays is presented. A high density poly(ethylene glycol) coating was deposited on glass slides as a background exhibiting low cell attachment properties. Phenylazide modified polymers were then printed on this background. UV irradiation of these polymer arrays resulted in the crosslinking of the polymer spots and their covalent attachment to the surface. Cell attachment was shown to follow the resultant surface chemistry pattern. Furthermore, the use of a robotic contact printer enabled the facile deposition of DNA microarrays on top of and aligned with the polymer microarrays. A transfected cell microarray was generated in this way, demonstrating not only the ability of this platform to limit cell attachment to specific regions, but the suitability for chip-based functional genomics, in particular, and high density cell assays in general.