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The decrease in the critical current density (Jc) of YBa2Cu3O7-x (YBCO) films with increasing film thickness was investigated for 0.2 - 2.4-μm-thick films grown on single crystal substrates. Microstructural and electrical properties were characterized by focused ion beam (FIB) microscopy, X-ray diffraction, energy dispersive X-ray spectroscopy in a field emission scanning electron microscope, atomic force microscopy, and current-voltage measurements at 77 K in self-field. FIB cross sections directly showed that the top 30% -40% thickness of YBCO films contained pores, misoriented YBCO grains, and Ba-rich second phase particles that collectively produced a "dead top layer" which is believed to limit the Jc of YBCO films thicker than 1 μm. A gas cluster ion beam etching and smoothing process partially removed the dead top layer and smoothed the film surface. In a 0.9-μm-thick YBCO film, removal of a 0.22-μm-thick dead layer yielded a 35% increase in Jc (up to 2.8 MA/cm2) and a 25% decrease in film roughness. In a 1.3-μm-thick YBCO film, removal of a 0.45-μm-thick dead layer yielded an 85% increase in Jc (up to 1.1 MA/cm2) and a 49% decrease in surface roughness. This study suggests that eliminating the dead top layer and smoothing the film surface might be key processing steps in the production of thick YBCO films with high Jc.