Purpose: Fibula free flap is currently used in mandibular reconstruction. The main difficulties involved in this surgery concern mandible shaping and therefore, osteotomy positioning on the fibula. The use of navigation could help in osteotomy positioning, but accurate registration is required. We assess a surface-matching method for fibula registration that relies on an iterative closest point (ICP) algorithm. Since the fibula shape is landmark free, a robust registration initialization approach is used to avoid non-optimal local minimums in the ICP. Methods: Bone surface-matching registration was evaluated on a 3D printed fibula and compared to its virtual reference model. The registration initialization relied on 3 initialization points placed on the surgically exposed area, geometrically remote from the fibular distal extremity. The bone surface was digitized, and the obtained point clouds were registered to the virtual reference model. The position of 3 assessment points engraved on the 3D printed fibula was then compared to that of the equivalent points on the virtual model. Results: The registration procedure was performed 24 times by an expert surgeon. Seventy-two target registration errors (TRE) were computed, corresponding to the distance between the paired assessment points. Most TRE (86.1%) were less than 1 mm, with a maximum of 1.552 mm. The overall mean value was 0.759 ± 0.302 mm. Conclusion: This study illustrates a surface-matching approach for fibula registration, with an initialization method based on points remote from the fibula distal extremity. This registration technique gave promising results and should be considered as a valid registration method for straight bones like the fibula. These findings indicate that navigation can be used for fibula flap shaping for mandibular reconstruction, with a noninvasive and accurate registration method.