Despite advances in nanomaterials synthesis, the bottom-up preparation of nanopattemed films as templates for spatially confined surface reactions remains a challenge. We report an approach to fabricating nanoscale thin film surface structures with periodicities on the order of 20 nm and with the capacity to localize reactions with small molecules and nanopartides. A block copolymer (BCP) of polystyrene-block-poly[(allyl glycidyl ether)-co-(ethylene oxide)] (PS-b-P(AGE-co-EO)) is used to prepare periodically ordered, reactive thin films. As proof-of-principle demonstrations of the versatility of the chemical functionalization, a small organic molecule, an amino acid, and ultrasmall silica nanopartides are selectively attached via thiol-ene click chemistry to the exposed P(AGE-co-EO) domains of the BCP thin film. Our approach employing click chemistry on the spatially confined reactive surfaces of a BCP thin film overcomes solvent incompatibilities typically encountered when synthetic polymers are functionalized with water-soluble molecules. Moreover, this post-assembly functionalization of a reactive thin film surface preserves the original patterning reduces the amount of required reactant, and leads to short reaction times. The demonstrated approach is expected to provide a new materials platform in applications including sensing, catalysis, pattern recognition, or microelectronics.