Disclosed is an anti-counterfeiting system. In a particular embodiment, the anti-counterfeiting system has a first structure having a plurality of three-dimensional nanostructures, each having a height dimension less than a wavelength of visible light. In addition, there is a second structure having a second plurality of three-dimensional nanostructures, each having a height dimension less than a wavelength of visible light. The first and second structures are configured to couple together. An alignment mechanism is operable to align the first structure to the second structure and establish proximate contact between the first and second pluralities of nanostructures. With respect to the first and second structures, each encodes part of an authentication key. The authentication key includes pre-determined elements and interaction modalities. The resolution of the structures makes them copy-resistant. An associated method of use is also provided.