Sapphire substrates, mechanically polished to an optical finish, were annealed for two days at either 1000°C or 1350°C. The near surface condition of as-polished and of the annealed substrates was analyzed by Rutherford backscattering/channeling (RBS-C) and by scanning electron microscopy/channeling (SEM-C), by transmission electron microscopy (TEM), and by scanning tunnelling microscopy (STM). The polished substrates were found to be RBS-amorphous up to 100 nm, and heavily damaged at larger depths. In agreement with these results, no electron channeling was obtained from polished samples. TEM, however, showed that the damaged region was crystalline, and the only defects detected were microtwins. Both RBS-C and SEM-C analyses revealed that the damage is removed when the sapphire substrates are annealed for 48 hrs. at 1350°C. The condition of the near-surface region, viz., as-polished or annealed, is found to strongly affect the morphology of the laser-irradiated copper films deposited on sapphire substrates. A correlation is found between the threshold for film evaporation and for film rupture upon laser irradiation, both being a function of the substrate condition. It is concluded that the near-surface damaged layer acts as a thermal barrier for heat transport across the substrate.