The effects of three in-situ pre growth substrate treatments on the quality of 3C-SiC epitaxial films on 6H-SiC(00.1) were evaluated by high resolution x-ray diffraction, synchrotron x-ray topography, atomic force microscopy, and optical microscopy. The Si-face substrates were etched in pure H-2, C2H4/H-2, or 0.5% HCl/H-2 mixtures to remove scratches and subsurface polishing damage prior to the 3C-SiC epitaxy by chemical vapor deposition. The dislocation density in the 3C-SiC thin films was estimated from the full width at half maximum (FWHM) of the x-ray diffraction rocking curves for a number of symmetric and asymmetric reflections. Etching in either C2H4 in H-2 or HCl in H-2 was more effective at producing smooth substrate surfaces than etching in pure H-2. The 3C-SiC films subsequently deposited on the smooth surfaces had shown a factor of ten reduction in the dislocation density compared to films deposited on substrates without pre growth surface treatments. The smoothest substrate surfaces produced the largest 3C-SiC domains and the lowest defect densities. Synchrotron x-ray topography of selected samples revealed cellular structure of dislocations, low angle grain boundaries and double positioning boundaries in the 3C-SiC films.