High temperature thermal treatment has been used to obtain atomically flat surfaces and to remove surface damage caused by mechanical polishing of as-received lithium niobate (LiNbO3) substrates. Annealing at 1000°C for 2 hours produces optimal surface smoothness. The micro steps are nearly parallel and periodic almost all over the sample. The step height on z-cut substrates was 0.212 nm, which was well in accordance with the distance between oxygen layers along the c-axis of the hexagonal unit cell of LiNbO3 crystals. The step terrace width is about 217 nm, and the surface roughness is 0.111 nm, for a 5 um x 5 um area unit. The authors grew high quality GaN films on these atomically-flat LiNbO3 substrates with AIN buffer layers using molecular beam epitaxy (MBE), and then investigated their structural properties. The full-width-at-half maximum (FWHM) value of the XRD (0002) GaN rocking curve was 122.14 arcsec for GaN film grown on the positive side of LiNbO3 substrates (+Z-LiNbO3. The morphology surface of GaN films was investigated using atomic force microscopy (AFM). The typical PL spectrum of GaN film grown on the both side of LiNbO3 substrate reveals a strong band-edge emission peak at 360 nm (3.45 eV).