Apical surgery for a mandibular molar is still challenging for many reasons. This report describes the applications of computer-guided cortical ‘bone-window technique’ using piezoelectric saws that prevented any nerve damage in performing endodontic microsurgery of a mandibular molar. A 49-year-old woman presented with gumboil on tooth #36 (previously endodontically treated tooth) and was diagnosed with chronic apical abscess. Periapical lesions were confirmed using cone-beam computed tomography (CBCT). Endodontic microsurgery for the mesial and distal roots of tooth #36 was planned. Following the transfer of data of the CBCT images and the scanned cast to an implant surgical planning program, data from both devices were merged. A surgical stent was designed, on the superimposed three-dimensional model, to guide the preparation of a cortical window on the buccal side of tooth #36. Endodontic microsurgery was performed with a printed surgical template. Minimal osteotomy was required and preservation of the buccal cortical plate rendered this endodontic surgery less traumatic. No postoperative complications such as mental nerve damage were reported. Window technique guided by a computer-aided design/computer-aided manufacture based surgical template can be considerably useful in endodontic microsurgery in complicated cases.