Aggregated asphaltene structural models have been generated through a molecular simulation geometry optimization process, using periodic boundary conditions. This methodology has been validated by first applying it to a pure aromatic system. Initially, a random distribution of 35 molecules was chosen and a geometry optimization process was performed, allowing the cell dimensions to vary without restrictions. The structure factor (S(k)) of an optimized final cell was obtained and compared with experimental results, and the agreement between theoretical and experimental S(k) profiles was satisfactory. This methodology was next used in the analysis of the morphology of 32 asphaltene model molecules and their aromatic cores; asphaltene model molecules were taken from literature. It is remarkable that face-to-face stacking of asphaltene aggregates was observed, as well as T-offset and T-shaped stacking geometries. Finally, the effect of aliphatic chains on the aggregates was also analyzed.