The polarized excitation of azobenzene molecules is frequently used to reorient the chromophores with their dipole transition moments migrating out of the polarization direction of the incident light. Such photoreorientation was shown to occur in molecular interface multilayer films of some amphiphilic azobenzene dyes on solid supports. In this study, the microscopic morphology and morphological changes on irradiation of such systems are investigated with atomic force microscopy (AFM), electron diffraction, and small angle X-ray reflection. It is found that the molecules are locally organized in patches of molecular layers, and AFM indicates that these film patches are crystalline. Macroscopically, freshly prepared films are organized in confluent stacks of these patches, and on irradiation, these structures segregate into confined domains with micron sizes, resembling two-dimensional polycrystals rather than coherent films. Unpolarized irradiation, accompanied with reorientation of the transition moments toward the surface normal, induces a reorganization of the molecules into structures with surface roughness values far above molecular dimensions, which does probably involve material transport over micron distances. Polarized irradiation, leading to in-plane reorientation of the molecules, does not affect the structure so drastically, and it is often difficult to discriminate illuminated from nonilluminated areas in the AFM.