Amphotropic copolymers containing rod-like side groups combine the ability to form Langmuir-Blodgett multilayer assemblies with thermotropic liquid crystalline selforganization on temperature changes. Photochromic azobenzene side groups affect the supramolecular structure in such copolymers in dependence on irradiation wavelength and polarization of the incident light beam as well as temperature. The aggregation phenomena at the polymer air interface caused by the amphotropic properties of the material were reversibly modified by the light induced variation of the molecular shape of the photochromic moieties. The vertically layered structure had been destroyed and rebuilt upon irradiation and annealing the LB films. Moreover, the optical in-plane anisotropy was erased on irradiation and reinduced using linearly polarized light. Combined investigations (angular dependent W-VIS measurements, energy dispersive SAXS and GID, high resolution AFM) provide new insights into the micromorphology as well as the surface structure of the condensed initial and transformed LB films.