Objectives: To assess: (1) the workflow in the treatment decision process of mandibular third molars based on a panoramic image and CBCT and (2) the impact of radiographic markers in CBCT on the decision to perform coronectomy. Methods: 1437 teeth in 917 patients (mean age 27.8 years, range 18–72) underwent clinical and panoramic examination. If there was an indication for removal of the tooth, and signs of a close relation to the inferior alveolar nerve were present in the panoramic image, a CBCT was performed. Treatment decision based on panoramic image and CBCT was calculated. Statistical analyses were performed to assess whether signs in CBCT had an impact on the treatment decision “coronectomy”. Moreover, the actually operated teeth and post-operative sensory disturbances were assessed and discussed in relation to the radiographic method. Results: Based on the panoramic image, in 462 cases it was decided not to treat, 553 were scheduled for surgery, and 422 referred for a CBCT examination. “No bony separation between the tooth and mandibular canal” seen in CBCT was the main factor influencing the decision to perform a coronectomy (odds ratio = 56.8, p < 0.001). 840 mandibular third molars had undergone surgical intervention, 152 had a coronectomy and 688 were fully removed. Six patients perceived a sensory disturbance of the inferior alveolar nerve: one permanent and five temporary. Conclusion: 29% of the examined cases were referred for a CBCT and of these, the majority were scheduled for coronectomy based on the sign “no bony separation between the tooth and mandibular canal” seen in CBCT.