As the three-dimensional (3D) reconstruction and visualisation of medical imaging systems, such as computed tomography (CT) and magnetic resonance imaging (MRI), become common approaches for assisting physicians with a visual representation of anatomy structures, a novelty approach adding functional elements of the human body started being explored. So, medical thermography has been used as a complementary imaging technique for diagnosis and monitoring of pathologies, based on the identification of surface temperature changes. Therefore, this paper presents a new open-source software approach to multimodal medical imaging. The proposed methodology involves the 3D reconstruction of an anatomical model and thermal model, being the latter based on a Structure from Motion (SfM) approach, and the combination of both models, providing a complete 3D multimodal model that contains inner information regarding the anatomy of the body, and outer physiological information. It showed efficient results regarding the visualisation of the multimodal model in a single coordinate system in different views (axial, coronal, and sagittal), allowing it to be inspected by physicians, whilst improving pathology assessment. The 3D multimodal models have potential to be expanded to medical applications, such as diagnosis, surgery, and follow-up care, whilst being cost effective by resorting to available open-source software.