In this paper, we illustrate the trapping effect of 2-D assembly of octa-alkoxyl-substituted phthalocyanine for individual molecules of phthalocyanine, prophyrins, and calix[8]arene. It is observed that single molecules are trapped in quadratic lattices rather than hexagonal lattices, and domain boundaries are preferential trapping sites as compared with the internal domain sites. The observed trapping behaviors could be considered in analogue to the phenomena of point defects, dislocations, and grain-boundary segregations in solid-state. materials.