Successful endodontic treatment depends on the effectiveness of the cleaning and shaping of the root canal system. Due to the complexity of the structure of root canal system and the particularity of root canal infections, the equipment and technology currently available for root canal preparation hinder the ability to adequately clean and shape the root canal system. In this review, we summarized the difficulties in the control of root canal infection, the new concept of three-dimensional root canal preparation, and its quality control and assessment.