A common problem in creating a finite element mesh is modeling the interface between incompatible element boundaries. Incompatibilities will arise in transitions between continuum and structural elements such as 3D solids and shells or in regions where edge to edge (or face to face) connectivity is not maintained. Presented here is a method implemented in the commercial structural analysis program, Applied Structure, to automatically handle these situations. Within the method, consideration is given to shell-to-shell, solid-to- solid, and shell-to-solid transitions. A theoretical background and several examples are given which illustrate the robustness of the method. Finally, some practical considerations are discussed with respect to typical applications of the approach.