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Background We compared the pre-operative 3D-surgical plan with the surgical outcome of complex two-stage secondary reconstruction of maxillofacial defects using inserted implants in the prefabricated fibula graft. Methods Eleven reconstructions of maxillofacial defects with prefabricated fibulas were performed using a 3D virtual planning. Accuracy of placement of the fibula grafts and dental implants was compared to pre-operative 3D virtual plans by superimposing pre-operative and post-operative CT-scans: we first superimposed the CT-scans on the antagonist jaw, to represent the outcome of occlusion, and then superimposed on the planned fibula segments. Results Superimposing the CT scans on the antagonist jaws revealed a median deviation of the fibula segments and implants of 4.7 mm (IQR:3–6.5 mm) and 5.5 mm (IQR:2.8–7 mm) from the planned position, respectively. Superimposing of the CT scans on the fibula segments revealed a median difference of fibula and implant placement of 0.3 mm (IQR:0–1.6 mm) and 2.2 mm (IQR:1.5–2.9 mm), respectively. Conclusions The final position of the fibula graft is determined by the occlusion of the denture, which is designed from the 3D plan. From a prosthodontic perspective, the accuracy of 3D-surgical planning of reconstruction of maxillofacial defects with a fibula graft and the implants allows for a favorable functional position of the implants and fibula graft. [ABSTRACT FROM AUTHOR]