High reynolds number flow simulations exhibit strong gradients normal to walls and across shear layers requiring much finer resolution of the solution in some directions compared to others. To keep mesh sizes manageable for such problems, meshes with highly anisotropic elements are necessary. In this paper, a method for generating boundary layer meshes for arbitrarily complex non-manifold geometric domains is discussed. A popular strategy for generation of boundary layers meshes is generalized to deal with non-manifold model topology as well as to generate better shaped elements. Results on complex configurations are presented to demonstrate the capabilities of the mesh generator.