Root canal treatment has advanced in recent years with the spread of microscopes. However, treating complex root canal systems remains difficult. Through an examination of examples from the literature and clinical practice, this paper discusses methods for isthmus and fin root canal enlargement and preparation design and root canal filling on the basis of the three areas of “anatomical complexity,” “root canal enlargement, preparation, and cleaning”, and “root canal filling.” Anatomical complexity: Isthmuses and fins have a high incidence and are present in more than 50% of mandibular molar mesial roots. However, the incidence drops as the root canal system matures with age, which means that age must also be taken into account during treatment. Root canal enlargement, preparation, and cleaning: Appropriate enlargement of the upper part of the root canal is necessary to enlarge and prepare isthmuses and other structures. Ultrasonic tip selection is also important during enlargement and preparation and the combined use of ultrasonic waves during root canal cleaning can enhance the cleaning effect. Root canal filling: The method of root canal filling needs to be chosen based on the site where an isthmus or fin has developed. Conclusions: No clear standards exist for the mechanical root canal enlargement, preparation, and root canal filling of anatomically complex sites, such as isthmuses and fins, and success largely depends on the surgeon’s knowledge and experience. Even if a microscope is used, appropriate treatment will not be possible without anatomical knowledge, techniques, and suitable tools. Treatment must be performed using a microscope and with the appropriate knowledge.
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