Carbon-based nanoparticles can significantly enhance the specific characteristics of polymers, impacting mechanical, thermal, electrical, and magnetic properties. However, incorporating these enhancements into final products can be challenging due to the influences of subsequent processing steps required to transform the material into components. This is the case of nano-modifications of 3D printing thermoplastic filaments. The filament characteristics and the printing process’s resulting material microstructure affect the final properties of the material produced. The resulting material exhibits a hierarchical multiscale structure, necessitating a combination of various simulation approaches and methods to capture the relevant effects and influences across different scales, ultimately allowing for accurate prediction of the final material response in the product. This study focuses on predicting key thermal and mechanical properties of polymer nanocomposites and 3D printing materials. The analysis is based on coarse-grained molecular dynamics and continuum models across different scales, complemented by experimental characterization of the base material (filament) and micrographic analysis of the printed material. The findings demonstrate the potential of modeling to predict various material responses. The multiscale model reveals that with a modest addition of nanofiller (up to 2 wt%), the Young’s modulus and thermal conductivity show up to 11% enhancement. These predictions closely align with the experiments, exhibiting a maximum deviation of 2.3%. In conclusion, this study demonstrates that the combination of diverse modeling techniques and experimental validation provides valuable guidance for materials development and engineering, as well as a deeper understanding of the process/structure/properties relationships.