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The nanostructure formation of the Stranski–Krastanow (SK) systems is investigated by simulating the surface undulation of the systems driven by the surface diffusion mechanism. Of particular interest is how the surface undulation leads to the development of faceted nanostructures and wetting layers. The results reveal that the development exhibits three common features in the coarsening SK systems, while the development also results in distinct film morphologies, controlled by the maximum surface coverage of faceted islands. The maximum surface coverage depends on the film thickness, the ratio between the two characteristic lengths of the SK system, and the effective surface energy density of flat film.