For decades, finite element analysis (FEA) has served as a ubiquitous tool, allowing engineers and scientists to gain critical insights into the behavior of complex composite materials. Despite the wide adoption of FEA, creating a conforming mesh for the most complex composite material models, such as mesoscale models of 3D textiles or microscale models of composites with reinforcement and irregular voids, remains a significant challenge. Much of the difficulty lies in the fact that many tools that create realistic surface geometries through process simulation often result in complex interpenetrations between objects. This paper proposes a pipeline of algorithms, some adopted from the visualization community and some novel, to automatically create a conforming, high-quality tetrahedral mesh for composite materials with complex geometries that may overlap. The details of a novel algorithm used to identify volume, surface, and edge features, while avoiding the use of a tolerance, are provided. Additionally, the paper describes three different methods to remove overlaps between tows. Finally, the algorithms are applied to a simple case with two orthogonal tows that overlap where they cross, demonstrating the result at each step and revealing the advantages and disadvantages of each of the three overlap removal algorithms.