Quantum dots (QDs) and quantum wires (QWRs) are promising for future optoelectronic device applications. To realize the expected performances of devices using such semiconductor nanostructures, the sites and sizes of the nanostructures must be effectively controlled. For this purpose, we have developed nano-fabrication technology using 'in situ electron-beam lithography' and self-organizing molecular-beam epitaxial growth. Using this method, fine holes were formed on GaAs surfaces, and then a few monolayers of InAs were supplied to form QDs. It was revealed that the resulting QDs were selectively formed in the holes, without any QD formation in the flat region between the holes, because of accumulation of In atoms in the holes. This result demonstrates the usefulness of the in situ patterning/self-organizing growth approach for realizing arbitrarily arranged nanostructures.