Although it is difficult to determine the atomic arrangement of boron, carbon, and oxygen in the solid clusters and oxides because of their low atomic number, it is believed that the high-resolution images should have “some” information for disordering, ordering, and doping atomic positions in these materials. In the present work, we obtained and predicted the information for disordering, ordering, and doping atomic positions in YB 56, HgTlBa 2CuO x, and N@C 60 from digital HREM images. Residual indices (R HREM = Σ ¦I obs − I cal¦/ ΣI obs) were used for image analysis. Difference images between observed and simulated images were also calculated for structure analysis. The present work indicates that this kind of atomic detection would be very useful for evaluation of local atomic positions in the crystal with light elements such as boron, carbon, nitrogen and oxygen atoms.