Purpose Osseointegrated skin-penetrating implants enhance the retention and stability of the craniofacial prostheses and provide the long-term comfort. However, to determine the implant locations is a great challenge facing the surgeon. Implants may either be located in conventional manner or by STL generated surgical guides. Materials and Methods Present study reports the CT based 3D virtual modeling, preoperative virtual planning and the implant placement by using a STL surgical guide, in an anotia case. Results Employed materials and the methods facilitated the implant surgery while improving the operational security. Conclusions CT based 3D virtual modeling of the surgical site, determining the implant locations virtually and the STL guided placement of the craniofacial implants, were found useful applications in order to facilitating the surgical intervention and providing prevention from complications.