A method for making multiple single molecule receptors in a nanopore structure includes depositing a first material and a second material by a physical vapor deposition (PVD) technique onto different selected interior surfaces of a nanochannel and functionalizing a surface of the first material, the second material, or both the first and second materials with a chemical compound having at least two functional groups. The first and second materials can be the same or different and form patches having diameters of about 1 to about 100 nanometers (nm). Also disclosed are embodiments of a nanopore structure including multiple single molecule receptors.