Focused ion beam (FIB) processing was performed to prepare an ultra-thin section of graft-copolymer of deproteinized natural rubber and polystyrene (DPNR-graft-PS), in order to obtain a three-dimensional (3D) image of the nanomatrix structure through transmission electron micro-tomography (TEMT) observation. The DPNR-graft-PS was immersed into OsO4 solution for more than 7 days for the sake of enhancing a contrast of the TEMT image during the FIB processing. In-situ observation with a field emission-scanning electron microscope was made during the FIB processing. The ultra-thin section prepared by FIB processing was compared with that prepared with a cryo-microtome in the TEMT observation. A distinctly clear TEMT image of the nanomatrix structure, comprising the natural rubber micro-particles and the nanomatrix of PS nano-particles/natural rubber, was obtained with the ultra-thin section prepared by FIB processing, but not with that prepared with the cryo-microtome. The FIB processing was proved to be indispensable for the TEMT observation of the nano-structure of the soft-materials. (C) 2014 Elsevier Ltd. All rights reserved.