The present invention provides high-density arrays including mask layers and methods of manufacturing the same. The arrays are formed on a polymeric substrate and include a mask layer. Various linking agents, linking agent coatings, and/or reactants may be provided on the mask layer. Where present, the linking agents and reactants preferably operate together to capture a desired analyte which can then be detected based on an electromagnetic signal, e.g., fluorescence, that is emitted by the analyte in response to excitation energy incident on the array. With the mask layer in place, the signal-to-background ratio provided by the arrays can be increased.