We report a comprehensive investigation on stacking faults (SFs) in the 3C-SiC cross-section epilayer. 3C-SiC growth was performed in a horizontal hot-wall chemical vapour deposition (CVD) reactor. After the growth (85 microns thick), the silicon substrate was completely melted inside the CVD chamber, obtaining free-standing 4 inch wafers. A structural characterization and distribution of SFs was performed by μ-Raman spectroscopy and room-temperature μ-photoluminescence. Two kinds of SFs, 4H-like and 6H-like, were identified near the removed silicon interface. Each kind of SFs shows a characteristic photoluminescence emission of the 4H-SiC and 6H-SiC located at 393 and 425 nm, respectively. 4H-like and 6H-like SFs show different distribution along film thickness. The reported results were discussed in relation with the experimental data and theoretical models present in the literature.