The highly dispersed metal (e.g. Au) nanoparticles have exhibited exceptional catalytic activity for several reactions, including CO oxidation. Their high catalytic activity has been attributed to nanoparticles nano-structural effects (including cluster thickness, shape, chemical information, and number of atoms of the cluster). The three dimensional exact structure and chemical bonding state of these supported nanoparticles is still challenging to be quantified by conventional methods due to their limitations in understanding size distribution of supported metal nanoparticles that are usually less than 1 nm (< 100 atoms). In this paper, the structure of Au heterogeneous catalysts has been successfully characterized by High Resolution Electron Microscopy (HREM), Z-contrast Scanning Transmission Electron Microscopy (STEM). The ligand protected Au13 nanoparticles on TiO2 support have been studied by ozone and thermal treatments to remove the ligands. The ozone removal method results in the truncated cuboctahedral structure while the thermal treatment results in the cuboctahedral structure. The ozone treatment yields less Au nanoparticles sintering than thermal treatment. Their FCC structure was confirmed by quantified Z-contrast STEM, HREM and its Fourier transformation.