The fundamental limitations associated with top-down lithographic techniques gradually have approached. One of methods to overcome these limitations is the combination technique of top-down nanofabrication such as nano imprint and bottom-up nanofabrication such as self-assembly. Nanoparticles has been expected to use as the building blocks. In order to realize this method, it is desirable to place nanometer sized components such as nanoparticles in exact positions for nano-fabrication with high precision and reproducibility. In particular, gold (Au) nanoparticles, which covalently linked to biomolecules such as DNA, peptides, nucleic acids, proteins, and cell have attracted much attention for biosensing, bioimaging, and plasmonics application, and so on. In this study, we present a simple method of controlled array of Au nanoparticles on a nanopattern by the combination of self-assembly techniques bottom-up nano-fabrication such as self-assembled monolayers and top-down nano-fabrication such as nano imprint. We believe this method will contribute to studies on the observation of single biomolecules such as DNA, peptides, nucleic acids, proteins, plasmonics and so on.