Secondary electron emission is developed as a means to quantify and image protein binding to Au surfaces modified with patterned organic thin-film arrays. Alkane thiols were patterned via microcontact printing on gold, and their effects on the secondary electron (SE) yield of the surface, systematically quantified. We show that a self-assembled monolayer (SAM) of hexadecane thiol significantly increases the SE yield over the native gold surface, a yield that increases as a function of alkane chain length (C8C16). This effect is linearly correlated with the surface potentials and wetting properties of these SAMs. Surface layers comprised of poly(ethylene glycol) (PEG) grafted polyacrylamide polymers behave differently, affecting the SE yield by attenuation according to the polymer thickness. These results demonstrate the relative contributions of factors related to the adsorbate molecular structures that serve to strongly mediate the SE yield, providing a foundation for exploiting them as a quantitative electron imaging probe. The latter capability is demonstrated using a model microfluidic assay in which a series of proteins was spatially addressed to a SAM-based pixel array. The gray scale contrasts seen with protein adsorption are directly correlated with both protein molecular weight and mass coverage. These methods are used in two model protein assay experiments: (1) the measurement of the concentration dependent adsorption isotherm for a model protein (fibrinogen); and (2) the selective recognition of a biotinylated protein layer by avidin. These results demonstrate a unique approach to imaging protein binding processes on surfaces with both high analytical and spatial sensitivity.