Finite element models of composite structures are generally shell-based and modeled at the laminate level. More detailed layer-by-layer lamina-level models are sometimes needed for representing joints or for modeling defect growth processes. We describe a method and toolkit for automating the creation and insertion of layerby-layer finite element sub-models of composite laminate. We focus in particular on representing damage captured from nondestructive evaluation (NDE) measurements. The method is based on scripting existing simulation and solid modeling tools (ABAQUS and ACIS). It works even on complicated, curved CAD models. The submodel location is identified by the intersection of a cylinder with the structure. We then execute a series of instructions to generate a new shell with the submodel region removed, generate the layer-by-layer submodel, and bond together the layers and models with desired boundary conditions and defects. The instructions represent the steps of lamination and bonding for creating the composite. The output of the method includes CAD models of the new shell and each lamina within the submodel, and a Python script for ABAQUS that will load the CAD models, bond them together, and apply the specified boundary conditions.