This work reports on the properties of cubic silicon carbide (3C-SiC) grown epitaxially on a patterned silicon substrate composed of squared inverted silicon pyramids (ISP). This compliant substrate prevents stacking faults, usually found at the SiC/Si interface, from reaching the surface. We investigated the effect of the size of the inverted pyramid on the epilayer quality. We noted that anti-phase boundaries (APBs) develop between adjacent faces of the pyramid and that the SiC/Si interfaces have the same polarity on both pyramid faces. The structure of the heterointerface was investigated. Moreover, due to the emergence of APB at the vertex of the pyramid, voids buried on the epilayer form. We demonstrated that careful control of the growth parameters allows modification of the height of the void and the density of APBs, improving SiC epitaxy quality.