Monolayer and bilayer structures of a nonplanar molecule, 5-(N,N-didecylamino)-2,4-pentadienal, physisorbed onto highly oriented pyrolytic graphite have been characterized using several scanning probe techniques, including scanning tunneling microscopy, and both contact and noncontact atomic force microscopy. These structures indicate several important components of this molecule in determining and enforcing an ordered packing motif that may be generalizable to other supramolecular design schemes. In the monolayer structure, the geometry of the amino group enforces a motif in which part of the molecule lies upon the graphite surface and one of the alkyl chains extends away from the surface. This extended chain is a structure director for the formation of bilayer structures. The apparent thickness and stability of the bilayer structures are shown to be dependent on the presence of water or other admixtures, suggesting intercalation of small, polar molecules into this bilayer.