Thorough debridement of the root canal system is essential for healing of apical periodontitis. Oval or ribbon shaped canals are difficult to clean; instruments tend to prepare the central part of the canal leaving unprepared buccal and lingual extensions (fins). Objectives: To compare three techniques for preparing oval shaped canals: anatomic endodontic technology (AET), hand (Hedström files) and rotary NiTi (EndoWave) instruments, with regard to untouched surface, remaining debris, canal shape, presence of fins and cross-sectional area. Methods: Three groups each of 13 extracted human mandibular premolars were used. After canal preparation, teeth were sectioned at three levels (coronal, middle, apical). Digital photographs of the root sections were used for scoring canal shape and fins, and histological sections were prepared for assessment of canal cleanliness and cross-sectional area. Results: Rotary NiTi resulted in significantly cleaner apical third compared to AET and hand instrumentation (P = 0.002 Kruskal-Wallis test). No significant difference was found among the three techniques with regard to untouched surface, cross-sectional area, remaining fins and canal shape at the three levels. None of the techniques resulted in completely prepared and cleaned canals. Conclusion: The new system (AET) did not perform better than rotary NiTi or hand instruments in oval shaped canals, and rotary NiTi gave the best results in the apical third.