The design and fitting of prosthetic sockets can significantly affect the acceptance of an artificial limb by persons with lower limb amputations. Clinical fitting is typically an iterative process, which requires patients’ feedback and professional assessment. When feedback is unreliable due to the patient’s physical or psychological conditions, quantitative measures can support decision-making. Specifically, monitoring the skin temperature of the residual limb can provide valuable information regarding unwanted mechanical stresses and reduced vascularization, which can lead to inflammation, skin sores and ulcerations. Multiple 2D images to examine a real-life 3D limb can be cumbersome and might only offer a partial assessment of critical areas. To overcome these issues, we developed a workflow for integrating thermographic information on the 3D scan of a residual limb, with intrinsic reconstruction quality measures. Specifically, workflow allows us to calculate a 3D thermal map of the skin of the stump at rest and after walking, and summarize this information with a single 3D differential map. The workflow was tested on a person with transtibial amputation, with a reconstruction accuracy lower than 3 mm, which is adequate for socket adaptation. We expect the workflow to improve socket acceptance and patients’ quality of life.