Porosity in functional oxide nanorods is a recently discovered new type of microstructure, which is not yet fully understood and still under evaluation for its impact on applications in catalysis and gas/ion storage. Here we explore the shape and distribution of pores in ceria in three dimensions using a modified algorithm of geometric tomography as a reliable tool for reconstructing defective and strained nanoobjects. The pores are confirmed as "negative-particle"or "inverse-particle"cuboctahedral shapes located exclusively beneath the flat surface of the rods separated via a sub-5 nm thin ceria wall from the outside. New findings also comprise elongated "negative-rod"defects, seen as embryonic nanotubes, and pores in cube-shaped ceria. Furthermore, we report near-sintering secondary heat treatment of nanorods and cubes, confirming persistence of pores beyond external surface rounding. We support our experiments with molecular modeling and predict that the growth history of voids is via diffusion and aggregation of atomic point defects. In addition, we use density functional theory to show that the relative stability of pore (shape) increases in the order "cuboidal"< "hexagonal-prismatic"< "octahedral". The results indicate that by engineering voids into nanorods, via a high-temperature postsynthetic heat treatment, a potential future alternative route of tuning catalytic activities might become possible.