In this work we investigated the influence of the Si substrate misorientation and 3C-SiC film thickness on the density of Anti-Phase Boundaries, in order to better understand the mechanism of antiphase domain annihilation. The two highlights in our work are the utilization of [001] orientated Si on-axis wafer with spherical dimples, which gave us access to a continuum of off-cut angles (0° to ~11° ) and directions, and the deposition of elongated silicon islands on the surface of 3C-SiC epilayers, which improved the detection of APDs by analysis of Scanning Electron Microscopy images. We found that for a given layer thickness the relative surface occupation of one domain increases with the off-cut angle value, leading to single domain film up to a certain angle. This critical value is reduced as the film is thickened.