Multilayer organic and inorganic systems of thin solid films are widely used in novel optoelectronic devices. The required properties of the system depend on the morphology of the films and transition zone at interfaces. We studied the formation of deposits of fluorinated azo-dyes, polymethine, merocyanine and sulfur-terminated organic compounds (STOC) by evaporation and condensation in vacuum. The films were deposited on glass, silicon (Si), gold (Au) and polytetrafluoroethylene (PTFE) substrates. The influence of dye chemical structure and substrate on deposit morphology was studied using atomic force microscopy (AFM). Depending on the ratio between thermodynamic and kinetic processes, islands, crystalline aggregates or nano-structures were obtained. A difference in the morphology of the same dye solid, but deposited on various substrates was detected. Changes in the dye end or side groups caused variation in the morphology of the dye solid film. STOC formed a smooth film on the Au surface, while on the glass and PTFE it formed various islands. Thin films of the dyes in PTFE matrix exhibited unique stability to action of external factors. A new type of evaporable dyes with unsaturated reactive bond at the end was synthesized. Using new evaporation-activation-polymerization methods, the films with enhanced hardness and thermal stability were prepared from new dyes. Several dyes formed nano-micro-wires during the self-assembly process, in some cases between two neighboring Au strips. Adjusting the structure of the molecule by changing the end groups allows purposeful control of the deposit morphology on the selected surface.