Separation of root canal instruments is a common incident during root canal treatments' procedures. The complex configuration of root canal systems is one of the most influencing factors, not only during the occurrence of instrument separation but also during the management of such unpleasant incidents. There are few reports on the management of fractured instruments located in the apical third of the root canals apical, especially those extruded beyond the apex. A 37-year-old woman was referred to an endodontic specialist to complete a root canal treatment after the separation of an endodontic file in the middle-third of the C-shaped root canal configuration (Vertucci type II) of the mandibular second molar. A failed attempt at managing the fragment by the dentist resulted in the backward placement of the fragment, which was more apically, and partial extrusion beyond the root apex. The fractured instrument was successfully and safely retrieved using different procedures and techniques including bypassing the fragment, loosening the fragment using ultrasonics and then removing it by the crab-claw shaped tweezers (Zumax broken instruments removal kit). This case report demonstrates the importance of high magnification provided by the dental operating microscopes and sound clinical skills and judgment, especially in assessing the difficulty of cases that is necessary for various treatment approaches. In addition, the availability of different armamentaria to manage separated instruments is essential. Finally, this case report proposes and advocates the idea of removing fractured instruments extruding beyond the apex without surgery.