INTRODUCTION: The purpose of this study was to evaluate the efficacy of three methods in removal of Resilon/new Epiphany self-etch (SE) soft resin endodontic obturation system. MATERIALS AND METHODS: Thirty extracted single rooted human teeth were prepared for endodontic treatment and obturated with Resilon/Epiphany SE. The roots were randomly divided into three groups; group 1 roots were retreated using Mtwo R/Mtwo files; group 2 were retreated using Mtwo R/Mtwo accompanied with chloroform; and group 3 were retreated using Mtwo R/Mtwo accompanied with Endosolv R. The cleanliness of canal walls was determined using scanning electron microscopy. Data were analyzed using ANOVA and LSD tests. RESULTS: Endosolv R combined with rotary files was more efficient in material removal compared to chloroform combined with rotary files and rotary files alone (P<0.05). Also, chloroform combined with rotary file was more efficient than rotary file alone in removing filling material from the root canals. Significant difference was found within group 1 between the coronal third compared to the middle and apical thirds (P<0.05). In group 2, there were more material remnants in the apical third (P<0.05). In group 3, there was no significant difference between the three segments of the root canals (P>0.05). CONCLUSION: All techniques left filling material remnants and debris on the root canal walls. Endosolv R combined with rotary files most effectively removed filling materials from the root canals, especially in the apical third.