A method of manufacturing a microarray includes providing a substrate having a surface that is immobilized with a functional group protected with an acid-labile protecting group and capable of coupling with an oligomer probe, providing a photoacid generator onto the substrate, disposing on the substrate an imprint template comprising a convex region and a plurality of concave regions surrounding the convex region so that the convex region contacts with or is adjacent to an upper surface of the substrate to define a plurality of reaction zones by the upper surface of the substrate and the convex region and the concave regions of the imprint template, exposing one or more of the reaction zones to light so that an acid is generated by the photoacid generator in the one or more exposed reaction zones and a functional group in the one or more exposed reaction zones is deprotected by the acid, and providing an oligomer probe onto the substrate so that the oligomer probe couples with the deprotected functional group.