We have used scanning tunneling microscopy, Auger electron spectroscopy, and low-energy electron diffraction to investigate the surface of Si(001) prepared by low-temperature thermal decomposition of an oxide layer and subsequent annealing in ultrahigh vacuum. Such a surface is found to roughen on the mesoscopic length scale and consists of 3000-Angstrom-wide voids of 2x1 reconstructed Si(001) surrounded by square-based pyramidal structures which are 200-300 Angstrom high and have a cusplike cross section. Atomic scale imaging and spectroscopy of the sides of the pyramids reveals a wide variety of vicinal surfaces as well as higher angle facets such as (3x2) reconstructed (113). The structure formed is independent of the original oxide thickness and is shown to be qualitatively different from that caused by deliberate carbon contamination of the surface. We propose that the pyramids are created by kinetic effects acting on the surface disorder caused by the oxide removal and represent a fundamental instability of the Si(001) surface. This has implications for molecular-beam epitaxy growth and device fabrication, as well as offering a lithography-free method of making Si nanostructures and a way of studying vicinal surfaces without complex sample preparation.