Scanning tunneling microscopy (STM) is used to probe the local atomic structure of the 6H-SiC(0 0 0 1) surface together with X-ray photoelectron spectroscopy (XPS) in UHV. We report STM observation of localized clusters assembled in an ordered (6 × 6) arrangement after annealing the (3 × 3) phase at 1000 °C. These clusters are round in shape and possess a diameter of 14.3 ± 0.5 Å and a height of 2.3 ± 0.2 Å. Further annealing of the surface beyond 1000 °C caused the clusters to disappear and we observed the formation of a (6 × 6) ring-like structure at 1050 °C. XPS data show that the surface is still Si rich, unlike the (6√3 × 6√3) phase or graphitic honeycomb structures which normally formed above this temperature. Observation of defect and cluster formation, as well as tetramer agglomeration, suggests the rearrangement of the (3 × 3) structure as temperature increases. STM is used to study this mechanism leading to the formation of (6 × 6) clusters. We propose a model utilizing Si tetra-cluster units as building blocks to elucidate the structure of the (6 × 6) clusters and explain the structural transformation observed.