The finite-element (FE) method is commonly used in biomedical engineering to simulate the behaviour of biological structures because of its ability to model complex shapes in a subject-specific manner. However, generating FE meshes from medical images remains a bottleneck. We present a template-based technique for semi-automatically generating FE meshes which is applicable to prospective studies of individual patients in which FE meshes must be generated from scans of the same structure taken at different points in time to study the effects of disease progression/regression. In this “template-based” meshing approach, the baseline FE (tetrahedral) volume mesh is first manually aligned with the follow-up images. The triangulated surface of the mesh is then automatically deformed to fit the imaged organ boundary. The deformed surface nodes are then smoothed using a Laplacian smoothing algorithm to correct triangle (surface nodes) distortion and thus preserve triangle quality. Finally, the internal mesh nodes are smoothed to correct distorted tetrahedral elements and thus preserve tetrahedral element quality. This template-based approach is shown to be as accurate and precise as the previous technique used by our group, while preserving element quality and volume.