Removal of a tumor in the oral cavity that has invaded into the bone may require the removal of a part of the bone, thereby losing continuity of the bone. The removal of the tumor including a required margin is 3D virtually planned in which the information of different imaging modalities is combined, such as CT and MRI. The surgical resection planning is translated to the operation room by designing patient specific surgical guides that uniquely fit the patient anatomy and indicate the virtually planned resection during surgery. Using these same techniques, a reconstruction of the bone using fibula bone can be 3D virtually planned and transferred to the operating room using a patient specific reconstruction guide.