Ni films are important as both Schottky junctions and Ohmic contacts for high temperature SiC devices. Ni/SiC Schottky junctions are observed to become Ohmic upon annealing. This transition has been attributed to changes in film microstructure. The experiments reported here compare the thermal behavior of Ni films deposited on standard 6H-SiC (0001) surfaces with films deposited on periodically stepped surfaces. The former were prepared by wet chemical etching and are typical of those used in device fabrication. The latter were prepared by high temperature hydrogen etching. Ni films ranging from monolayer to nominal device thickness (~50 nm) were annealed on both surfaces. Analysis of these surfaces by in-situ Auger electron spectroscopy (AES) and ex-situ atomic force microscopy (AFM) provided elemental, chemical and morphological information. The results show that the morphology and microstructure of annealed films are dependent on initial film thickness and substrate surface conditions.