Dentinal microcracks formed during apical resection may lead to increased susceptibility to root fracture and improper sealing of apical preparation that may negatively influence the outcome of endodontic microsurgery. This study was performed to analyze the root-end surface for dentinal microcracks using a scanning electron microscope (SEM) after resection with high-speed bur and trephine drill. Thirty extracted single-rooted maxillary premolar teeth were selected and randomly distributed into two groups (n = 15). Working length was established using a #15 K-type file. Canals were prepared with a rotary Ni-Ti system to size 30/0.06 using endomotor, irrigated with 3% sodium hypochlorite, dried with paper points, and obturated with gutta-percha cones using a single-cone technique. All samples were mounted on preformed molds and poured using a mixture of sawdust and gypsum. In Group A; tungsten carbide bur was used to perform a freehand apicoectomy. In Group B; a trephine drill was used with a three-dimensional guide to perform 3 mm of root resection. Apicoectomy was performed in both groups under a dental operating microscope. Resected root ends were inspected for microcracks using SEM. The Shapiro-Wilk and Mann-Whitney U-test were used for statistical analysis. Microcracks were observed in all samples in both study groups. Trephine drill produced more microcracks on the resected root surface compared to the use of high-speed tungsten carbide bur with a statistically significant difference (P < 0.05). The trephine drill used during targeted endodontic microsurgery produced more microcracks on the resected root dentine surface compared to the high-speed tungsten carbide bur used during freehand apicoectomy.