The present study evaluated the obturation quality of root canals filled with BioRoot RCS sealer and single gutta-percha point by undergraduate student (US), postgraduate student (PS) and endodontist (ED). Twenty-one plastic models of upper premolars were enlarged with HyFlex EDM instruments to a size 40/0.04 taper and randomly divided into three groups (7 teeth/14 canals per group): US, PS and ED. After the obturation of root canals with BioRoot RCS and one HyFlex EDM size 40 gutta-percha point, plastic models were scanned using micro-computed tomography scanner (µCT) SkyScan 1272 at isotropic resolution of 10 µm. The porosity distribution was evaluated separately for the apical, middle and coronal thirds. The Kruskal–Wallis, Mann–Whitney, Friedman and Wilcoxon tests with the significance level set at 5% were used for data analysis. The µCT evaluation revealed open pores being the dominant type of porosity in all experimental groups and root canal thirds, with the highest percentage of pores in the apical third of root canal fillings. The quality and homogeneity of single cone root canals fillings remained similar between the groups in the apical and middle thirds (p > 0.05). Significant differences were observed only in the coronal third (p < 0.05).