Surgical osteotomy guides created by computer-aided design/computer-aided manufacturing (CAD/CAM) have been developed and are now widely used in maxillofacial reconstruction. However, there are no standard procedures for dealing with an intraoperative change in defect size. We report on a case in which we used our CAD/CAM guides to deal with an intraoperative change in defect size in a maxillary reconstruction. We planned the maxillary reconstruction using a free fibula flap because of left maxillary sinus cancer in a 73-year-old man. In Japan, we cannot use commercially supplied CAD/CAM guides because these have not been approved by the government. We created novel CAD/CAM guides by using free software and a low-cost 3D printer. We performed model surgery to check the accuracy of the design and to prebend the titanium plates before the operation. The actual defect in the maxilla was found to be smaller than that used in preoperative planning. It was therefore necessary to rearrange the fibular segments and to rebend the plates. Comparison between the preoperative and postoperative 3D images showed that the deviation was 2–4 mm. In case that the CAD/CAM guides become inapplicable because of an intraoperative change in defect size, rearranging both the ends of set-up fibular segments and rebending the plates in situ allows us to deal with the situation. However, because extra time is needed to rearrange and rebend, the total operation and flap ischemic times are not shortened.