The J-aggregation phenomenon of cyanine dyes has important commercial applications in the photographic industry. A typical cyanine dye was appended to poly-l-lysine in order to stabilize its J-aggregation at the molecular level. Molecular modeling was used to provide information on the conformation of the dye-polymer formed. Possible orientations of poly-l-lysine with cyanine dyes appended to it based on molecular modeling calculations and physical measurements are discussed and evidence for a beta -pleated sheet conformation of the poly-l-lysine is shown. Also, for the first time J-aggregated monomer dyes and dye-polymers are used to build layer-by-layer assemblies in combination with inorganic clay sheets. The newly created architectures are used to fabricate three-dimensional structures on a solid support and have potential applications in building layered systems for optical signal processing. Microscopy measurements provide information about the organization of the J-aggregated cyanine dye-clay composites on solid supports.