Reverse Monte Carlo (RMC) modeling, based on diffraction data, was applied to various kinds of amorphous materials to visualizing the three-dimensional atomic arrangement and to elucidate topological characteristics. For an as-grown amorphous carbon nanocoil, it could be clarified that graphene sheets are winding and the regular ABAB… stacking is lost and the configuration gradually changes to the hexagonal network with great regularity through heat treatment. Voronoi analysis of the RMC model could characterize the atomic configurations for NiZr2 and CuZr2 metallic glasses. The Zr environments are very similar in the two systems, but there are marked differences between the polyhedra around Ni and Cu atoms. The polyhedra around Ni atoms are dominated by prismatic-like polyhedra. In contrast, icosahedron-like polyhedra are preferred for Cu.