Objectives: This study had the objective to determine the percentage of gutta-percha filled area (PGFA) obtained by two techniques (Thermafil and System B) associating scanning electron microscopy (SEM) and the digital processing of images. Methods: Forty five first inferior molars were accessed, conventionally prepared and filled as following: G1: Lateral Condensation- Control group(n=15); G2: System B (n=15) e G3: Thermafil (n=15). Transversal cuts were made at 4 and 6 mm from the apex of all teeth. The samples were prepared for observation under a SEM and photomicrographs were made with magnifications between 15X and 60X. Through digital processing and analysis of the obtained images, the total root canal area and the total area occupied by gutta-percha were measured, and this way the PGFA of every group was calculated.Results: The PGFA values found at 4 mm were: G1 (80,3 ± 11,7); G2 (84,9 ± 9,6) e G3 (98,86 ± 2,12). The data obtained at 6mm were: G1 (85,2± 7,7); G2 (89,9 ± 6,64) e G3 (98,91 ± 1,22). Such information was statistically treated using Friedman and Wilcoxon Signed-Rank non-parametric tests. Statistical evaluation revealed significant differences between G3 and G2-G1 (P< .01). No statistical significant difference was observed between G2 and (P> .05).Conclusion: Considering our results, it is possible to conclude that the Thermafil system produced significantly superior PGFAs compared to the other groups, suggesting a more homogeneous obturation.