Abstract Anti-counterfeiting tags are a simple and easy way to avoid duplication/forgery of valuable products; however, counterfeiting has evolved over time, with the help of newer technologies to clone and reproduce exact signatures, tags, barcodes, etc that are difficult to identify. To prevent such counterfeiting, it is imperative to obtain advanced and encoded anti-counterfeiting technologies with constant research and innovation. With this motivation, we have designed a sub-micron-scale patterned, fluorescent anti-counterfeiting tag based on an emissive layer embedded in a non-emissive polymer layer. The fabrication of the embedded structure is achieved using step-by-step writing of emissive and non-emissive layers using two-photon lithography. Interestingly, the encoded message is visible under ultraviolet illumination, and the structure is invisible under white light illumination. The proposed method can be extended for multilayer patterning with spatial positioning of different encoded messages along the height of the structure to incorporate layered security.