Nanoscale chemical patterning of different chemical species (amine, thiol, aldehyde, and biotin) in independent nanopatterns is achieved by the iterative application of thermochemical nanolithography (TCNL) to inscribe amine patterns followed by their chemical conversion to other functional groups. Due to the unique chemical stability of the patterns, the resultant substrates can be stored for weeks and subsequently be used for covalent and molecular-recognition-based attachment of nano-objects using standard chemical protocols. In particular, the ability of this methods to attach proteins and DNA to the chemical nanopatterns and to create co-patterns of two distinctive bioactive proteins is demonstrated.