The creation of distinct, periodically structured vicinal Si(1 1 1) and (1 0 0) substrates has been studied using scanning tunnelling microscopy at various temperatures. The vicinal Si(1 1 1) and (1 0 0) surfaces transform under heat treatment in a self-organised way into flat and stepped regions. Optical and electron beam lithography is used to produce a regular hole pattern on the surfaces, which interferes with the temperature-driven morphological changes. The step motions are strongly influenced by this pre-patterning. Pre-patterned Si(1 1 1) surfaces transform into regular one-dimensional (1D) and two-dimensional (2D) morphologies, which consist of terraces and arrangements of step bunches and facets. On pre-patterned Si(1 0 0) substrates different re-organisations were observed where checkerboard-like 2D structures are obtained. (C) 2004 Elsevier B.V. All rights reserved.