The fluorescence characteristics and the topography of domains of J-aggregates formed by the thiacarbocyanine dye THIATS (3,3'-disulfopropyl-5,5'-dichloro-9-ethylthiacarbocyanine) adsorbed onto a dioctadecyldimethylammonium bromide (DODAB) layer and deposited on a solid substrate were studied using confocal fluorescence microscopy and atomic force microscopy (AFM). The fluorescence and topography of the films reveal a one-to-one correlation for the domains formed by the adsorbed cyanine dyes. The packing of the dye molecules in the bulk of the domains remains unchanged after deposition. The thickness of the dye layer, determined by atomic force microscopy, confirms that only a single dye layer, wherein the dye molecules have an edge-on orientation, is deposited in these domains. The influence of the deposition process (Langmuir-Blodgett or Langmuir-Schaefer) is mostly limited to the amphiphile regions between the two-dimensional dye crystals and to the rim of the two-dimensional dye crystals. For the film deposited using the Langmuir-Blodgett technique, the aggregation was disturbed at the rim of the quasi-circular domains. Dye material was however deposited as indicated by the monomer fluorescence. Polarization experiments revealed a random orientation for the dye molecules at the rim, in contrast with the polarization effect observed for the bulk of the domains. The film deposited using the Langmuir-Schaefer technique seems to remain structured at the rim of the domains. For these films, deposited on a hydrophobic substrate, however, the packing of the DODAB material between the domains undergoes drastic changes as shown by the AFM experiments. Due to the decreased stability outside the domains collapse of the DODAB film occurs. Fluorescence spectra could be collected at different positions of the domains, revealing whether the dye molecules were present as monomer or J-aggregates.