In this work, polystyrene (PS) and boron nitrides nanotubes (BNNT) composites were fabricated, prepared, and characterized using modified direct mixing and sonication processes. The polymer composites were extruded into filaments (BNNTs at 10 wt. %) for 3D printing, utilizing the fused deposition modeling (FDM) technique to fabricate parts for mechanical and thermal applications. Using a direct mixing process, we found that the thermal conductivity and the mechanical strength of the PS-BNNT composite were respectively four times and two times higher compared to the sonication method. The thermal stability and glass transition temperatures were positively affected. A 2D microstructural mechanical entanglement model captured the exact geometry of the nanotubes using the MultiMechanics software, and the performance of the additive manufactured (AM) PS-BNNT composites part for thermomechanical application was simulated in COMSOL. The modified direct mixing process for PS-BNNT, which affects morphology, proved to be effective in achieving better interfacial bonding, indicating that BNNTs are promising fillers for improving thermal and mechanical properties, and are applicable for thermal management and electronic packaging.