Metal oxide semiconductor (MOS) structures containing nanocrystals are fabricated by using rapid thermal oxidations of amorphous silicon films. The amorphous films are deposited either by electron beam deposition method or by electron beam deposition assisted by Ar ion beam during deposition. Post oxidation of e-beam deposited film results in relatively small hysteresis of capacitance-voltage (C-V) and the flat band voltage shift, $DeltaV_{FB}$ is less than 1V indicative of the formation of low density nanocrystals in $SiO_2$ near $SiO_2$/Si interface. By contrast, we observe very large hysteresis in C-V characteristics for oxidized ion-beam assisted e-beam deposited sample. The flat band voltage shift is larger than 22V and the hysteresis becomes even broader as increasing injection times of holes at accumulation condition and electrons at inversion condition. The result indicates the formation of slow traps in $SiO_2$ near $SiO_2$/Si interface which might be related to large density nanocrystals. Roughly estimated trap density is $1{ imes}10^{13}cm^{-2}$. Such a large hysteresis may be explained in terms of the activation of adatom migration by Ar ion during deposition. The activated migration may increase nucleation rate of Si nuclei in amorphous Si matrix. During post oxidation process, nuclei grow into nanocrystals. Therefore, ion beam assistance during deposition may be very feasible for MOS structure containing nanocrystals with large density which is a basic building block for single electron memory device.