The creation and local reorganisation of periodically structured Si(111) substrates is described. A regular hole pattern is produced on vicinal Si(111) surfaces by lithographic techniques. After heat treatment this pre-structured Si surface transforms into terraced and stepped regions. The resulting terrace size can be controlled by the layout of the hole pattern. The early stage of the structural changes were studied by scanning tunnelling microscopy and secondary electron microscopy as a function of the annealing temperature and for different dimensions of the hole pattern. A simple model is proposed which ascribes the observed morphological changes to an anisotropic surface diffusion on the patterned surface. It is proposed that the variation of the hole diameter and spacing between holes can be employed to control systematically the resulting surface structure after heat treatment.