We studied the range over which inhomogeneous interfacial strain influences the hetero-epitaxial growth of Ge layers on variously modified Si(001) substrates which result from the insertion of a thin (4.2A) Ge-layer, giving a Si/Ge/Si superstructure. A 2xN periodic array of dimer vacancies is buried in the Ge-layer and creates an elastic perturbation in the top Si-layer. This interfacial strain modifies the growth of subsequent Ge-layers. The critical thickness for the transition between smooth (2D) and corrugated (3D self-assembled Ge hut-clusters) morphology are controlled by the Si-overlayer thickness.