An array of troughs was prepared on a 6H-SiC(0001) surface using focused ion beam (FIB) patterning. Troughs were etched with various ion doses and close-to-circular voids of increasing depths for larger ion doses were obtained. The samples were then etched in a hot-wall reactor at a hydrogen partial pressure of 13 mbar at 1800 ^°C. The resulting morphological reorganizations have been studied by scanning electron and atomic force microscopy. Very regular hexagonal voids with facets oriented perpendicular to the surface were obtained after hydrogen etching. The voids were surrounded by regular secondary facets of lower inclination. Whereas the depth of the voids increases with ion dose, the void diameter and facet sizes stay constant. This effect is explained by surface diffusion during hydrogen etching. The FIB technique in combination with hydrogen etching allows the preparation of very regular surface patterns and highly ordered wells and tubes for nanometer-sized sieves and photonic crystals.