We studied the orientation of the hexagonal columnar mesophase formed by self-organization of a perfluorinated supramolecular dendrimer containing a carboxyl (-COOH) headgroup and three perfluorinated (-CF3) tails at surfaces modified with self-assembled monolayers (SAMs). The SAM-modified surfaces studied were composed of an Au(111) substrate modified with one of five types of SAM. The SAM molecules used all had an -SH headgroup, but different terminal groups, (-CF3, -CH3, and -OH) and different spacer chain lengths. Atomic force microscopy (AFM), transmission electron microscopy (TEW and contact angle microscopy results revealed that the lattice parameters and structure of the perfluorinated supramolecular dendrimer are retained, but the orientation of the columns is strongly affected by the characteristics of the SAM surface. The supramolecular columns took on a planar alignment on the -CF3 and -OH terminated SAM surfaces, but exhibited a perpendicular orientation on the -CH3 terminated SAM surface. These variations in column alignment can be attributed to the types of molecular interactions between the terminal groups of the SAM molecules and the perfluorinated core/tails of the supramolecular columns. However, the surface morphology and orientation was not affected by changing the space chain length of the SAM molecules used.