Methods for producing ligand substrates and arrays, e.g., peptide and nucleic acid arrays, as well as the arrays produced thereby, methods for use of the arrays and kits that include the same are provided. In the subject methods, a substrate having a surface displaying photocleavable functional groups that produce surface bound photocleavage produced functional groups upon irradiation is first provided, where the photocleavable groups are then cleaved to produce a surface that displays desired functional groups. The resultant substrates, optionally after an additional functionalization step, are then contacted with ligands or monomeric precursors thereof, e.g., via deposition of each different ligand onto a different region of the surface, resulting in covalent attachment of the contacted ligands to the surface. The subject methods find use in the preparation of a variety of different types of arrays, where the produced arrays find use in a variety of different applications, including both genomic and proteomic applications.