Provided is a sensor array and a method of forming the same. The sensor array includes an array of apertures etched into a 3D patterned resist layer to expose areas of one or more agents and/or reagents deposited on a substrate. The sensor is formed using a Self-Aligned Imprint Lithography (“SAIL”) method, a process that allows for a one-time deposition of all required materials followed by a series of etching/cleaning steps. The location of reagents on the sensor template, as well as the concentration gradient of each reagent, may be controlled through the sensor manufacturing process. Bores of a single reagent, or bores containing two or more reagents, may be formed using the SAIL process.