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Objective The 3D printed medical models can come from virtual digital resources, like CT scanning. Nevertheless, the accuracy of CT scanning technology is limited, which is 1mm. In this situation, the collected data is not exactly the same as the real structure and there might be some errors causing the print to fail. This study presents a common and practical way to process the skull data to make the structures correctly. And then we make a skull model through 3D printing technology, which is useful for medical students to understand the complex structure of skull. Materials and MethodsThe skull data is collected by the CT scan. To get a corrected medical model, the computer-assisted image processing goes with the combination of five 3D manipulation tools: Mimics, 3ds Max, Geomagic, Mudbox and Meshmixer, to reconstruct the digital model and repair it. Subsequently, we utilize a low-cost desktop 3D printer, Ultimaker2, with polylactide filament (PLA) material to print the model and paint it based on the atlas. Result After the restoration and repairing, we eliminate the errors and repair the model by adding the missing parts of the uploaded data within 6 hours. Then we print it and compare the model with the cadaveric skull from frontal, left, right and anterior views respectively. The printed model can show the same structures and also the details of the skull clearly and is a good alternative of the cadaveric skull. Conclusion We present an available and cost-effective way to obtain a printed skull model from the original CT data, which has a considerable economic and social benefit for the medical education. The steps of the data processing can be performed easily. The cost for the 3D printed model is also low. The manipulation procedure presented in this study can be applied widely in processing skull data.