The use of focused ion-beam ͑FIB͒ nanopatterning for manipulating self-assembled ZnO nanodots is described. Highly aligned ZnO-nanodot arrays with various periodicities ͑e.g., 750, 190, and 100 nm͒ on FIB-nanopatterned SiO 2 / Si substrates were prepared by metal-organic chemical-vapor deposition ͑MOCVD͒. The artificially assembled ZnO nanodots had an amorphous structure. Ga atoms incorporated into the surface areas of FIB-patterned nanoholes during FIB engraving were found to play an important role in the artificial control of ZnO, resulting in the production of ZnO nanodots on the FIB-nanopatterned areas. The nanodots evolved into single-crystalline dot clusters and rods with increasing MOCVD-growth time. In addition, microphotoluminescence measurements showed that the ZnO-nanodot arrays have low-dimensional quantum characteristics.