Usual rubber products are a composite from rubber and nano-filler (e.g. silica, carbon black, etc.), and it is believed that the good dispersion of the nano-filler is the most important issue determining the performance of rubber vulcanizates. So far, transmission electron microscopy (TEM) has been the most useful tool for evaluation of the dispersion. However, it affords images of the sample projected on an x, y-plane, and the information along the thickness (z-axis) direction is missing. Three-dimensional (3D) visualization of nanometer structure of nano-filler dispersion in a rubber matrix is what all rubber technologists have been dreaming of. This dream is at last realized, and described in this paper. Use of TEM combined with computerized tomography (abbreviated as 3D-TEM in this paper, which is sometimes called electron tomography) enabled us to reconstruct 3D images of nano-filler (silica or carbon black) aggregates in rubbery matrix. It is said that nano-filler aggregate is a structure of size from 10 nm to 1000 nm, and agglomerate is an even larger structure. The 3D-TEM results on silica aggregates in natural rubber were presented in this paper. Silica aggregates were characterized by combining the 3D images of the vulcanizates. Furthermore, density of silica loaded natural rubber as an example of physical properties, was measured, and explained by the structure elucidated by 3D-TEM.