Disclosed is a method of preparing a biosensor that involves providing a substrate including a surface having a topographical pattern formed at one or more sites on or in the surface, coating the substrate with a solution including hydrogel particles, wherein the hydrogel particles self-assemble on the surface to mask the surface except at the one or more sites, and binding one or more capture molecules to the one or more sites to form the biosensor. Systems that include the biosensor, as well as methods of using the biosensor, are also disclosed.