The microstructural and compositional evolution of thick (>1 μm) high temperature superconducting YBa 2 Cu 3 O 7 - x (YBCO) films grown on single crystal SrTiO 3 substrates by the metal organic chemical vapor deposition (MOCVD) process was investigated by focused ion beam microscopy, scanning electron microscopy, energy dispersive X-ray spectroscopy, X-ray diffraction, and atomic force microscopy. This study showed that as the MOCVD YBCO film thickness increased above 0.5 μm, defects such as second phase particles, pores, and misaligned grains preferentially nucleated and grew at the YBCO surface. A portion of this defective top layer was eliminated from all the samples using a gas cluster ion beam (GCIB) process that first removed material with a focused argon cluster beam. Next, an oxygen cluster beam was used to smooth the surface and re-oxygenate the YBCO. Comparing the critical current (I c ) measured before and after GCIB processing showed that the I c remained the same, and even improved, when part of the defective top layer was removed. This microstructural and electromagnetic ''dead layer'' is believed to be responsible for the overall I c decrease of MOCVD YBCO films thicker than 0.5 μm.