We report on the modifications in morphology and microscopic structure induced by photoexcitation of homo- and heterostructures of a side chain liquid crystalline polymer, namely a polyacrylate with an azobenzene moiety in the side chain. The structures were molecular mono- and multilayers deposited with the Langmuir-Schaefer technique. The structural and morphological determinations were performed with synchrotron radiation Xray reflectometry and Grazing Incidence Diffraction (GID). We observe extensive photoinduced effects on the nanoscale: expansion of the multilayers independently of number of layers, reduction of surface toughness, and destruction of order to yield a glasslike phase. The study of superlattices composed of alternate layers of barium behenate and our polymer indicates a general reduction of photoinduced structural effects on the polymer multilayer. Finally, we discuss these effects as a function of temperature from the range of the glass transition to the clearing point.