PURPOSE: Virtual reality (VR) simulation is an effective training system for medical residents, allowing them to gain and improve upon surgical skills in a realistic environment while also receiving feedback on their performance. Percutaneous nephrolithotomy is the most common surgical treatment for the removal of renal stones. We propose a workflow to generate 3D soft tissue and bone models from computed tomography (CT) images, to be used and validated in a VR nephrolithotomy simulator. METHODS: Venous, delay, non-contrast, and full body CT scans were registered and segmented to generate 3D models of the abdominal organs, skin, and bone. These models were decimated and re-meshed into low-polygon versions while maintaining anatomical accuracy. The models were integrated into a nephrolithotomy simulator with haptic feedback and scoring metrics. Urology surgical experts assessed the simulator and its validity through a questionnaire based on a 5-point Likert scale. RESULTS: The workflow produced soft tissue and bone models from patient CT scans, which were integrated into the simulator. Surgeon responses indicated level 3 and above for face validity and level 4 and above for all other aspects of medical simulation validity: content, construct, and criterion. CONCLUSION: We designed an effective workflow to generate 3D models from CT scans using open source and modelling software. The low resolution of these models allowed integration in a VR simulator for visualization and haptic feedback, while anatomical accuracy was maintained.