A thermodynamically driven self-organization of microclusters of semiconductor nanocrystals with a narrow size distribution into periodic two-dimensional (2D) arrays is an attractive low-cost technique for the fabrication of 2D photonic crystals. We have found that CdSe/ZnS core/shell quantum dots or quantum rods, transferred in aqueous phase after capping with the bifunctional surface-active agent DL-cysteine, form on a poly-L-lysine coated surface homogeneously sized micro-particles, droplet-like spheroid clusters and hexagon-like colloidal crystals self-organized into millimetre-sized 2D hexagonal assemblies. The presence of an organic molecular layer around the micro-particles prevents immediate contact between them, forming an interstitial space which may be varied in thickness by changing the origin of the molecular layer capping nanocrystals. Due to the high refractive index of CdSe and the low refractive index of the interstitial spaces, these structures are expected to have deep gaps in their photonic band, forming hierarchically ordered 2D arrays of potentially photonic materials.