Herein, we report the fabrication, characterization, and testing of a polymer microprojection array, for the direct and selective capture of circulating biomarkers from the skin of live mice. First, we modified polycarbonate wafers using an electrophilic aromatic substitution reaction with nitric acid to insert aromatic nitro-groups into the benzene rings, followed by treatment with sodium borohydride to reduce the nitro-groups to primary amines. Initial characterization by ultraviolet–visible (UV–vis) spectroscopy suggested that increasing acid concentration led to increased depth of material modification and that this was associated with decreased surface hardness and slight changes in surface roughness. Chemical analysis with X-ray photoelectron spectroscopy (XPS) and attenuated total reflectance fourier transform infrared (ATR-FT-IR) spectroscopy showed nitrogen species present at the surface for all acid concentrations used, but subsurface nitrogen species were only observed at acid concentrations >35%. The nitrogen species were identified as a mixture of nitro, imine, and amine groups, and following reduction, there was sufficient amounts of primary amine groups for covalent attachment of a polyethylene glycol antifouling layer and protein capture probes, as determined by colorimetric and radiometric assays. Finally, the modification scheme was applied to polycarbonate microprojection arrays, and we show that these devices achieve flank skin penetration depths and biomarker yields comparable with our previously reported gold-coated silicon arrays, with very low nonspecific binding even in 10% mouse serum (in vitro) or directly in mouse skin (in vivo). This study is the first demonstration showing the potential utility of polymer microprojections in immunodiagnostics applications.