Despite the latest advancement made in its techniques and devices/apparatuses and the resulting rising expectation in the field of dental surgery, apicoectomy performed in the molar teeth remains a technical challenge and lacks evidence substantiated by long-term follow-up studies. This study sought to investigate the treatment outcomes and post-operative success rate in the root-end resected molar teeth accompanied by a high level of surgical risks due to their close proximity to the mandibular canal and maxillary sinus. A total of 68 patients who received treatment at Livingwell Dental Hospital between 2004 and 2010 and underwent apical surgery in the maxillary or mandibular molar area were enrolled in this study. A total of 160 roots collected from 75 molar teeth were subjected to surgical endodontic treatment and subsequently evaluated clinically as well as radiographically. Based on the results of the study, the clinical success rate was found to be 78.8% in cases involving radiological healing. Likewise, 90.7% of the roots recorded a robust clinical survival rate, but with incomplete healing as shown by radiography. The results indicate that the apical procedure involving molar teeth is a prognosis-friendly method that promises positive outcomes and higher success rate based on long-term follow-up observations.