The use of virtual surgical planning (VSP) and computer-aided design and manufacturing to assist in osseous reconstruction has become the standard of care in head and neck reconstruction. The use of the free fibula flap with VSP remains the most common flap for osseous reconstruction, and as such, it is well described in the published literature. The scapular free flap (SFF) based on the angular branch has not yet garnered the same attention. The popularity of the SFF osseus head and neck reconstruction is increasing due to the flaps' inherently different properties and indications it can fulfill; the natural curvature of the bone, the reduced incidence of atheroscelerosis in the donor vessels and the earlier postoperative mobilization of the patient. In the preoperative planning process, the SFF presents several unique challenges and considerations that differ from the free fibula flap. It is important for surgeons already using, or considering using the SFF, that VSP is used correctly to achieve optimal outcomes. The authors aim to describe and clarify aspects of VSP use in SFF reconstruction in the head and neck area with a specific focus on: (1) The perforator-like vascular anatomy of the scapula; (2) How to maximize the shape of the scapula to minimize osteotomies; (3) Fine-tuning of scapula osteotomies on side table; (4) How to plan cutting guide placement and fit on the scapula. The authors hope that this article will help reconstructive microsurgeons plan and perform the SFF in conjunction with VSP.