A novel method was developed for fabricating nanopatterns embedded on micropillar-structured surfaces using nanowelding technology for security identification. Commonly used substrates, that is, polyethylene films, glass wafers, Si wafers, and curved surfaces, were employed and their characteristics were evaluated. Cr was deposited onto the selected substrate to strengthen the adhesion force, and an adhesive layer of ultra-thin metal was deposited on top of the Cr layer. Lastly, nanopatterns were embedded on the substrates by nanowelding. The morphologies, cross sections, and three-dimensional (3D) images of the fabricated nanostructures were evaluated, and their crystalline structures and compositions were analyzed. Using the same method, nanopatterns embedded on micropillar-structured surfaces were fabricated for the first time as security patterns to improve security identification. The fabricated security patterns were characterized in three stages. First, micropillar structures and structural color were simply observed via optical microscopy to achieve a preliminary judgment. The appearance of structural color was due to the nanostructures fabricated on the micropillar surface. Next, the designed nanopatterns on the micropillar-structured surfaces were observed by scanning electron microscopy. Lastly, the changes in the spectral peaks were precisely observed using a spectrometer to achieve an enhanced security pattern. The fabricated security patterns can be suitable for valuable products, such as branded wines, watches, and bags. In addition, the proposed method offers a simple approach for transferring metal nanopatterns to common substrates. Moreover, the fabricated security patterns can have potential applications in semiconductor electrodes, transparent electrodes, and security identification codes.