Structure formation of a perfluoroalkyl terminated liquid crystal molecule was studied by molecular dynamics simulations. Two distinct structures with smectic-C-like layers and with bundles (blocks) of collapsed layers were spontaneously formed depending on the simulation temperatures. The bundles in the latter structure were somewhat positionally ordered (with respect to the small angle spots in its structure function) and orientationally isotropic overall even though the molecules making each bundle were well oriented. These characteristics of the simulated system well correspond to the cubic phase of the real system, and an even more precisely correspond to the proposed cubic structure model [M. Yoneya, E. Nishikawa, and H. Yokoyama, J. Chem. Phys. 120, 3699 (2004)] with respect to its hierarchical structure. (C) 2004 American Institute of Physics.