The 2D structures of a variety of n-alkyl-substituted perylene diimides adsorbed onto HOPG and MoS2 surfaces from phenyloctane solutions were studied using scanning tunneling microscopy (STM). Both rectangular, or herringbone-like, structures and row structures were observed. Surprisingly, the lattice constants, and thus the area per molecule of the rectangular structures, did not increase as expected when the alkyl chain length was increased. Protrusion of the alkyl tails into the solvent above the 2D layer is proposed to account for this behavior. Row structures, where the alkyl tails lie flat on the substrate surface, were also observed wherein the area per molecule increases as expected for the increase in the length of the alkyl tail. The formation of domains with a particular orientation with respect to the underlying lattice was observed for many of the 2D structures. The alignment of the molecular layers with the substrate could be explained with a point-on-line coincidence model. Formation and filling of missing molecule defects within the oriented domains was observed during continuous scanning of the STM.