GaAs microcrystal growth and its position control was demonstrated using a low energy focused ion beam system to fabricate the photonic crystals. Due to the rapid progress in ULSI design and the trend in high density packing, in the near future, the Al or Cu based interconnection system will face a difficulty in the signal flow. For this purpose, the photonic crystal and its application to the optical signal transfer system has been intensively studied. In this system, a crucial point is how to fabricate the ordered and controlled structure which has higher dielectric constant. For this system, imbedded GaAs microcrystals in SiO2 are thought to be the best candidate. But the challenging is the position controlling of the GaAs microcrystals. For this purpose, we demonstrate the array of GaAs microcrystals on Si(100) surface with As-termination method.