To investigate the effect of surface patterning on island growth, a real-time study by scanning tunneling microscopy (STM) of Ge deposition on nanostructured Si(001) surfaces is presented. The substrate is nanopatterned by the STM tip and the subsequent evolution of a Ge layer deposited at 500 °C is recorded. The formation of the wetting layer, a transition stage and the growth of three-dimensional (3D) Ge huts are examined dynamically. The 2D-3D transition is described in terms of the nucleation and evolution of pre-pyramids consisting of (001) oriented terraces, which eventually transform into pyramids by successive introduction of {105} facets. Substrate patterning strongly affects the positioning of 3D islands, and represents a route toward ordering of Ge islands.