We have used atomic force microscopy (AFM) to study the effect of common substrate surface treatments for the metal-organic chemical vapor deposition (MOCVD) of GaN on sapphire. It appears that contaminants play a major role in the surface chemistry and strongly influence the morphology of the treated surfaces. In order to investigate the role of these contaminants, we have introduced the concept of “controlled contamination” (CC), namely, exposure of the sapphire surfaces to controlled amounts of potential contaminants in-situ and investigation of the resulting sapphire morphology. The results showed that sapphire, considered to be a very stable oxide surface, is clearly reactive in the GaN MOCVD chemical environment at the high temperatures (HT) employed, allowing us to use CC for obtaining sapphire substrates with controlled roughness. Nevertheless, epitaxial growth using the two-step GaN MOCVD process appears to be very robust and practically insensitive to the (submicronscale) substrate morphology.