The morphological evolution of both pits and SiGe islands on patterned Si(001) substrates is investigated. With increasing Si buffer layer thickness the patterned holes transform into multifaceted pits before evolving into inverted truncated pyramids. SiGe island formation and evolution are studied by systematically varying the Ge coverage and pit spacing and quantitative data on the influence of the pattern periodicity on the SiGe island volume are presented. The presence of pits allows the fabrication of uniform island arrays with any of their equilibrium shapes.