The aim of this study was to determine the percentage of gutta-percha-filled area (GPFA) obtained by Thermafil and System B techniques using light microscopy and digital image processing. Forty-five human mandibular first molars were prepared and obturated as follows: Group 1: lateral condensation (n = 15); Group 2: System B (n = 15); and Group 3: Thermafil system (n = 15). Horizontal sections were cut 4 and 6 mm from the apical foramen of each tooth. The samples were metallographically prepared and taken through photomicrographs. Using digital analysis, the cross-sectional area of the canal and the gutta-percha areas were measured. The GPFA data obtained for the three groups were analysed using the non-parametric Friedman and Wilcoxon Signed-Ranks tests. Significant differences were found between Group 3 and Group 2-Group 1. No significant difference was found between Group 2 and Group 1. The Thermafil system produced significantly higher GPFAs than lateral condensation and System B techniques (P < 0.01). This result suggests that the Thermafil system can reduce sealer and voids.