To evaluate the effectiveness of the ProTaper and Mtwo retreatment systems for removal of resin-based obturation techniques during retreatment. A total of 160 maxillary anterior teeth were enlarged to size 30 using ProTaper and Mtwo rotary instruments. Teeth were randomly divided into eight groups. Resilon+Epiphany, gutta-percha+Epiphany, gutta-percha+AH Plus and gutta-percha+Kerr Pulp Canal Sealer (PCS) combinations were used for obturation. ProTaper and Mtwo retreatment files were used for removal of root canal treatments. After clearing the roots, the teeth were split vertically into halves, and the cleanliness of the canal walls was determined by scanning electron microscopy. Specimens obturated with gutta-percha and Kerr PCS displayed significantly more remnant obturation material than did specimens filled with resin-based obturation materials. Teeth prepared with Mtwo instruments contained significantly more remnant filling material than did teeth prepared with ProTaper. ProTaper files were significantly faster than Mtwo instruments in terms of the mean time of retreatment and time required to reach working length. The Resilon+Epiphany and AH Plus+gutta-percha obturation materials were removed more easily than were the Epiphany+gutta-percha and Kerr PCS+gutta-percha obturation materials. Although ProTaper retreatment files worked faster than did Mtwo retreatment files in terms of removing root canal obturation materials, both retreatment systems are effective, reliable and fast.