The rehabilitation of the skull’s bones is a difficult process that poses a challenge to the surgical team. Due to the range of design methods and the availability of materials, the main concerns are the implant design and material selection. Mirror-image reconstruction is one of the widely used implant reconstruction techniques, but it is not a feasible option in asymmetrical regions. The ideal design approach and material should result in an implant outcome that is compact, easy to fit, resilient, and provides the perfect aesthetic and functional outcomes irrespective of the location. The design technique for the making of the personalized implant must be easy to use and independent of the defect’s position on the skull. As a result, this article proposes a hybrid system that incorporates computer tomography acquisition, an adaptive design (or modeling) scheme, computational analysis, and accuracy assessment. The newly developed hybrid approach aims to obtain ideal cranial implants that are unique to each patient and defect. Polyetheretherketone (PEEK) is chosen to fabricate the implant because it is a viable alternative to titanium implants for personalized implants, and because it is simpler to use, lighter, and sturdy enough to shield the brain. The aesthetic result or the fitting accuracy is adequate, with a maximum deviation of 0.59 mm in the outside direction. The results of the biomechanical analysis demonstrate that the maximum Von Mises stress (8.15 MPa), Von Mises strain (0.002), and deformation (0.18 mm) are all extremely low, and the factor of safety is reasonably high, highlighting the implant’s load resistance potential and safety under high loading. Moreover, the time it takes to develop an implant model for any cranial defect using the proposed modeling scheme is very fast, at around one hour. This study illustrates that the utilized 3D reconstruction method and PEEK material would minimize time-consuming alterations while also improving the implant’s fit, stability, and strength.