Zinc oxide (ZnO) bulk single crystals, which are of high purity and transparency with a large size of 2 in., are successfully grown by the hydrothermal method. The sliced substrates are chemomechanically polished to form an epi-ready surface. The impurities existing on the as-polished substrate surface are characterized before and after annealing by SIMS (secondary-ion mass spectroscopy), and a damaged surface layer due to chemomechanical polishing is evaluated by an optical method. We attempt to remove the layer damaged due to chemomechanical polishing with two approaches, chemical etching and thermal annealing in N 2, O 2 or high vacuum. The improvement of the surface morphology and crystallinity is evaluated by means of high resolution X-ray diffraction (XRD), photoluminescence (PL) and atomic force microscopy (AFM). In the PL measurements, the relative intensity of the first-order longitudinal optical phonon replica of the free exciton (FX-1LO) is compared against varying etching depth. The relative intensity becomes weak with increasing etch depth and finally saturates at the etch depth of 5 μm. After the annealing process, we grow ZnO thin films on these ZnO(0001) substrates by plasma-assisted molecular beam epitaxy. Films grown directly on the substrate show a 3D growth mode in the initial stage of growth with various surface treatments. To overcome this problem, we employ a low temperature grown ZnO buffer layer (LT-ZnO), and a two-dimensionally grown high quality ZnO film is attained.