Metal and semiconductor nanoparticles attract much interest owing to their specific properties because they are expected as next generation electronic materials for display and LED, catalyst of solar cells, fluorescent marker in medical field, color material, optical limiter and so on. In particular, metal nanoparticle is expected as small-sized electronic devices such as single electron transistors, biosensing application and so on. In order to develop novel devices and biosensing application, it is essential to construct ordered structure of the nanoparticles on solid substrate. In particular, gold (Au) and silver nanoparticles, which covalently linked to biomolecules such as DNA, peptides, nucleic acids, proteins, and cell have attracted much attention for biosensing and bioimaging application. In this study, the location control of nanoparticles was successfully performed by the combination of top-down nano-fabrication such as lithography and bottom-up nano-fabrication such as self-assembly. The number of Au nanoparticle attatchment to water-soluble dithiol SAMs can be easily controlled by the length of SAMs.