A continuous phase field simulation is carried out to study the strain-mediated patterning of surface nanostructure by the subsurface island array. It is interesting to find that there exists a competition between the contributions to the self-organized process from the non-uniform surface stress and subsurface island array. Numerical simulations demonstrate that a tailored surface nanostructure can be obtained by tuning the inhomogeneous strain distribution induced by the subsurface island array, which is sensitive to the misfit strain, spacer layer thickness, geometry and spacing of embedded islands. The local self-assembling process of surface islands recovered from our numerical results is in agreement with the observation made in the recent experiments on the Ge/Si system with subsurface Ge islands array. (C) 2004 Elsevier B.V. All rights reserved.