Organic nanostructured materials are of increasing interest for applications in the fields of bioanalysis, photocatalysis, photonics, and organic light-emitting diodes. However, their preparation is still difficult to control and their optical properties are inadequately known. A solvent-exchange process called the “reprecipitation method” was used here to prepare nano- and microcrystals from fluorescent dyes belonging, for example, to the coumarin and nitrobenzoxadiazole (NBD) series. Typically, the dyes were dissolved in a hydrophilic organic solvent and then suddenly placed in an aqueous environment, where they spontaneously produce molecular assemblies. According to the self-association properties of the dyes and to the experimental conditions used, the nano- and microcrystals obtained exhibited different sizes and shapes, as observed by fluorescence and electron microscopy. In some cases, the crystal habit was controlled by adding some additives to the reprecipitation medium. The overall optical properties of the free-standing particles in suspension were generally quite close to those of the dissolved dyes. However, strong distortions of the absorption and emission spectra were observed for crystals grown in the presence of ionic additives. Under the fluorescence microscope, individual microcrystals may show peculiar emission characteristics, displaying bright and dark zones, or behaving like tiny optical fibers.