FePt nanoparticles of uniform sizes, compositions, and crystal structures can be obtained by chemical synthesis. Additionally, the nanoparticles can be well dispersed by the adsorption of a surfactant on the nanoparticle surface. Previously, the immobilization of FePt nanoparticles on a thermal oxide Si substrate was carried out by chemical synthesis, utilizing the PtS bonding between the -SH functional group in (3-mercaptopropyl)trimethoxysilane, MPTMS and Pt in FePt nanoparticles. However, controlling FePt nanoparticle arrays by this synthesis method was very difficult. In the present study, we attempted to control the distortion of the arrangement of FePt nanoparticles using an MPTMS layer modified with a silane coupling reaction and a geometrical structure prepared by ultraviolet nanoimprint lithography (UV-NIL). In this study, the hole-patterns used for the geometrical structure on Si(1 0 0) were 200 nm wide, 40 nm deep, and had a 500 nm pitch. The 5.6 nm FePt nanoparticles were used to coat the hole-patterns by using a picoliter pipette. An XHR-SEM image clearly revealed that the FePt nanoparticles were successfully arranged as a single layer with an average pitch of 10.0 nm by PtS bonding in the hole-patterns on Si(1 0 0). © 2010 Elsevier B.V. All rights reserved.