Finite element simulations in domains with strong gradients across thin sections typically require meshes with multiple elements through these sections to accurately capture the solution. Most of the published techniques for isotropic mesh generation are not suited for the creation of such meshes in general, arbitrarily complex, non-manifold domains. In this paper an automatic method is described for identification of thin sections of a domain and anisotropic refinement of an initial mesh to introduce a user-requested number of elements through the thin sections. The method uses local mesh modification operations to effect the refinement and subsequent realignment of edges along the thickness direction and perpendicular to it. Results are presented for a number of general models to illustrate the capability of the mesh generator.