This paper deals with Finite Element (FE) modeling of human body structures. More specifically, it focuses on the FE mesh generation process, which is a long and tedious task in the case of irregular and non-homogeneous structures. Whereas for regular and symmetrical bodies (like in the architectural domain for example), some automatic mesh generators have been developed, no robust system is provided for living structures, which are, by definition, non-homogeneous, irregular and patient-specific. This paper proposes a new algorithm, called the mesh-matching (M-M) algorithm, that automatically generates patient-specific 3D meshes for FE models of structures with complex geometry. It assumes that the shape which is studied is sufficiently close to a known “standard” model for which a mesh has been already generated by an expert. The algorithm proposes then to use a registration method, in order to infer the “standard” finite element mesh to the data. The M-M algorithm is tested and initially validated on five human femurs.