The bilayer stripe patterns formed by long-chain alkane derivatives on graphite provide a unique opportunity for the study of molecular adsorption, aggregation, and reaction on patterns with confinement size less than 10 nm. Fatty acids, such as arachidic acid (AA), self-assemble on graphite into a sheet of parallel stripes with periodicity at the scale of the molecular chain length (5.6 nm for AA). Thus the molecular pattern is defined precisely by the size and functionality of the headgroup and tailgroup of the amphiphile. Molecular patterns formed by fatty acid salts, also called metal soaps, allow the precise control of the number and location of the metal ion, and can serve as molecular templates for the synthesis of semiconductor nanocrystal arrays. In order to understand the effect of the metal ion, we carried out atomic force microscopy (AFM) and Fourier transform infrared spectroscopy (FTIR) investigations of AA's self-assembly in the presence of various metal ions including Mn(II), Fe(II), Co(II), Ni(II), Cu(II), Zn(II), Cd(II), and Fe(III). We found that the stripe orientation is dictated by the graphite lattice, the stripe periodicity is determined by the AA chain length, and the size, shape, and degree of order of the stripe crystalline domain are influenced by the bonding strength of the metal ion to the carboxylic ligand. The change of morphology in the self-assembled pattern shows a trend along the Irving-Williams series.