The face is the initial feature used to judge gender in public spaces; it is also a source of significant gender dysphoria. Surgical techniques are available for non-cisgender male patients who desire a more masculine face by augmenting certain features to change the bony framework of the skull. Augmentation using virtually designed patient-specific polyetheretherketone implants has now become a more widely applied method in maxillofacial surgery. When designing implants for augmentation, a three-dimensional (3D) reference or template is very useful. Hence, a 3D statistical shape model was developed of a male skull shape from information from a population of 40 male patients containing the mean shape and principal components of shape variation. By overlaying the template and the patient's 3D skull model, this method identified the regions of gender dimorphism in this case to be the orbital ridge, zygomatic regions, and frontal bossing area. Based on the 3D template overlay, polyetheretherketone augmentation implants were virtually designed in close consultation with a patient to augment the aforementioned regions. The virtual statistical shape modeling template offered an objective reference, and the possibility to fully involve the patient in the treatment planning.