Background: The aim of this study was to investigate intraoperative methods to generate patient-specific PMMA bone implants during a craniotomy. The proposed methods combine a cost-efficient, and non-invasive structured light scanner (SLS) as an imaging modality and a prototype printer for rapid generation of implant molds. Methods: This simulation study was performed using retrospective data from three craniotomy patients. The extracted bone flap and the cranial defect were scanned using a SLS, which generates a 3D surface model of an object by projecting a series of light-patterns on it. Prototype printed implant models were generated using two different techniques. The molds were then used to shape PMMA bone implants. These implants were evaluated regarding their accuracy to reconstruct the natural skull anatomy and compared to freehand formed implants. Results: The patient-specific bone implants reconstructed the preoperative anatomy with an average RMS error of 1.37mm (StDev 0.27), compared to an error of 1.5mm (StDev 0.43) for the freehand shaped implants. On average the intraoperative scanning time was 4.7min. The average time to generate and print the implant molds was 204 min. Conclusions: Results of this study have shown great promise for the proposed method to be used for patient-specific bone flap reconstruction during craniotomies.