Ll0-FePt nanoparticle having high magnetic anisotropy is a promising candidate for the future ultra high magnetic recording material. We have succeeded in the fabrication of cubical FePt nanoparticles. It is necessary for high areal recording density to develop a homogeneous assembled technique of the cubical nanoparticle with its magnetic easy axis in the vertical direction on a substrate. It has been known the selective chemical reaction between metal species and functional group of organic molecules. We focused on the selective chemical reaction to control the direction of the magnetic easy axis in the cubical nanoparticle. In this study, the modification of the organic molecule with various functional groups to the surface of the cubical nanoparticle was examined. Consequently, the amino groups were replaced by thiol groups and carboxyl groups on the surface ligands of the nanoparticle were residual, and then, we confirmed bonding thiol group end to Pt atom selectively.