The influence of prior electron beam irradiation on the growth of island structure on a silicon wafer was investigated. The substrate was irradiated by a finely focused electron beam scanning along a line. It was found that the islands tended to avoid growing (just) on the irradiated traces on the substrate. This is due to the creation of contamination pattern on the substrate surface by the electron beam irradiation. The phenomenon has been applied to provide a nanometer scale island structure in the form of a prescibed square lattice on the substrate.