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Endodontic microsurgery (EMS) techniques have increased success rates over traditional approaches. Despite surgical advances, anatomically challenging scenarios can preclude EMS in certain cases. The aim of this article was to introduce targeted EMS, which uses 3-dimensional–printed surgical guides (3DSGs) and trephine burs to achieve single-step osteotomy, root-end resection, and biopsy in complex cases. In each of 3 cases, a 3DSG with a trephine port was printed using computer-aided design/computer-aided manufacturing implant planning software. The osteotomy site, angulation, and depth of preparation were defined preoperatively to avoid sensitive anatomic structures. The 3DSG was inserted at the target site to achieve precise osteotomy and root-end resection during surgery. A hollow trephine rotated within the 3DSG port produced single-step osteotomy, root-end resection, and biopsy. Root-end preparation and fill were accomplished, and tissues were sutured in place. Targeted EMS potentiated successful surgical treatment in 3 anatomically challenging scenarios: (1) a palatal approach to the palatal root of a maxillary second molar, (2) a facial approach to a fused distofacial-palatal root of a maxillary first molar, and (3) a mandibular second premolar in close proximity to the mental foramen. Trephine burs guided by 3DSGs produce efficient targeted osteotomies with a predictable site, angulation, and depth of preparation. Apical surgery in challenging anatomic cases such as the palatal root of the maxillary second molar, fused molar roots, and root ends in approximation to the mental nerve are possible with targeted EMS.