Additive manufacturing (AM) is revolutionizing how we create things, offering innovative solutions that rival traditional manufacturing methods. In Fused Filament Fabrication (FFF), incorporating continuous fiber-reinforced filaments has significantly enhanced mechanical properties, making them valuable across diverse sectors like aerospace, automotive, and robotics. However, before printing a part, numerical simulation for design verification is essential. Yet, there’s a lack of suitable tools for modeling the complex material properties, particularly for composite lattice structures. To address this, we propose a three-level periodic homogenization method. The first level focuses on modeling individual filaments, followed by characterizing inter-bead voids at the second level, and finally, modeling collective lattice behavior at the third level. Hexagonal cellular lattice composite structures were modeled and tested to confirm the method’s accuracy and its value in supporting simulation and modular design for the composite FFF process.