Herein we report the topochemical modification of polymer surfaces with perfluorinated aromatic azides. The aryl azides, which have quaternary amine or aldehyde functional groups, were linked to the surface of the polymer by UV irradiation. The polymer substrates used in this study were cyclic olefin copolymer and poly(methyl methacrylate). These substrates were characterized before and after modification using reflection-absorption infrared spectroscopy, sessile water contact angle measurements, and X-ray photoelectron spectroscopy. Analysis of the surface confirmed the presence of aromatic groups with aldehyde or quaternary amine functionality. Enzyme immobilization and patterning onto polymer surfaces were studied using confocal microscopy. Enzymatic digests of protein were carried out on modified probes manufactured from thermoplastic substrates, and the resulting peptide analysis was completed using matrix-assisted laser desorption/ionization mass spectrometry. The use of functionalized perfluorinated aromatic azides allows the surface chemistry of thermoplastics to be tailored for specific lab-on-a-chip applications.