Laminated fiber-reinforced polymer (FRP) composites are widely used in aerospace and automotive industries due to their combined properties of high strength and low weight. However, owing to their complex structure, it is difficult to assess the impact of manufacturing defects and service damage on their residual life. Non-destructive evaluation (NDE) of composites using ultrasonic testing (UT) can identify the presence of defects. However, manually incorporating the damage in a CAD model of a multi-layered composite structure and evaluating its structural integrity is a tedious process. We have developed an automated framework to create a layered 3D CAD model of a composite structure and automatically preprocess it for structural finite element (FE) analysis. In addition, we can incorporate flaws and known composite damage automatically into this CAD model. The framework generates a layer-by-layer 3D structural CAD model of the composite laminate, replicating its manufacturing process. The framework can create non-trivial composite structures such as those that include stiffeners. Outlines of structural defects, such as delaminations detected using UT of the laminate, are incorporated into the CAD model between the appropriate layers. The framework is also capable of incorporating fiber/matrix cracking, another common defect observed in fiber-reinforced composites. Finally, the framework can preprocess the resulting 3D CAD models with defects for direct structural analysis by automatically applying the appropriate boundary conditions. In this paper, we show a working proof-of-concept of the framework with capabilities of creating composite structures with stiffeners, incorporating delaminations between the composite layers, and automatically preprocessing the CAD model for finite element structural analysis. The framework will ultimately aid in accurately assessing the residual life of the composite and making informed decisions regarding repairs.