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The nanostructure formation effected by the surface undulation on the Stranski-Krastanow (SK) systems during the annealing process is investigated by simulating the morphological evolution of the systems driven by surface diffusion. The results reveal three common features in the formation process. First, the essence of the nanostructure formation is the transformation of the film material above the wetting layer into faceted islands. Second, the wetting layer thickness is given by the first critical thickness for the SK transition. Third, the width of the nanostructures measured at the average film height is close to a constant during the formation process.