This study on future ultrahigh density magnetic recording devices aims to develop a technique for arranging FePt nanocubes on a substrate by using organosilane as an interlayer. An array of FePt nanocubes was formed by chemical synthesis, utilizing the Pt-S binding between the SH functional group in (3-mercaptopropyl)trimethoxysilane and Pt in the FePt nanocubes. The morphology of the FePt nanocube array on the substrate was characterized using atomic force microscopy and plan-view scanning electron microscopy, which revealed that the array was a monolayer. After SiO2 was coated by chemical vapor deposition as a protective layer for sintering prevention, annealing was carried out at 900 degrees C for 3 h in a reducing atmosphere to transform the crystal structure of the FePt nanocubes to the L1(0) phase. X-ray diffraction results revealed that the annealed FePt nanocube array had a FePt(110) orientation and L1(0) phases such as (001) and (110). The Pt-S binding did not obstruct the L1(0) ordering of FePt. Consequently, a method for arranging nanoparticles by using the organic molecules with functional groups that can interact with nanoparticle selectivity as an interlayer can be applied as a formation technique for arranging a wide range of nanoparticles. (C) 2010 The Electrochemical Society. [DOI:10.1149/1.3465631] All rights reserved.