Unlike existing methods that rely on manual procedures for repairing finite element meshes in computer-based simulations, embodiments automatically repair finite element meshes for use in simulations of real-world objects. One such embodiment begins by identifying a non-compliant mesh element in a finite element mesh and extracting a mesh patch from the finite element mesh that includes the identified non-compliant mesh element. To continue, an invariant patch description for the extracted mesh patch is generated and a repair solution corresponding to the generated invariant patch description is obtained from a database storing pre-determined repair solutions. In turn, the mesh patch in the finite element mesh is repaired using the obtained repair solution.