In this work, different multilayer conformations of a linear amphiphilic molecule, octadecylphosphonic acid (OPA), were investigated by atomic force microscopy (AFM), X-ray reflectivity, and X-ray diffraction. It was found that these molecules spontaneously pack into well-organized self-assembled bilayers (SABs) when the structures are formed inside concentrated solutions and/or after slow solvent evaporation. The molecular structure of an OPA SAB was observed to be dependent on its position along a stack of bilayers: when the SAB is at, or close to, the stack surface, OPA molecules are vertically aligned and form 5 nm thick bilayers; when it is in the middle of a stack of hundreds, or thousands, of bilayers, OPA molecules are tilted and form 3.4 nm thick bilayers. The van der Waals interactions among the long OPA alkyl chains were used to explain and also predict some features of the molecular arrangement inside both bilayer types. Using the AFM technique, which also enabled the application of pressure onto a bilayer surface, oblique and hexagonal molecular packings were observed, probably corresponding to both 5 and 3.4 nm thick bilayers, respectively.