Carbon Nanotubes (CNTs)-polymer composites are promising candidates for a myriad of applications. Ad-hoc CNTs-polymer composite fabrication techniques inherently pose roadblock to optimized processing resulting in microstructural defects i.e., void formation, poor interfacial adhesion, wettability, and agglomeration of CNTs inside the polymer matrix. Although improvement in the microstructures can be achieved via additional processing steps such as-mechanical methods and/or chemical functionalization, the resulting composites are somewhat limited in structural and functional performances. Here, we demonstrate that 3D printing technique like-direct ink writing offers improved processing of CNTs-polymer composites. The shear-induced flow of an engineered nanocomposite ink through the micronozzle offers some benefits including reducing the number of voids within the epoxy, improving CNTs dispersion and adhesion with epoxy, and partially aligns the CNTs. Such microstructural changes result in superior mechanical performance and heat transfer in the composites compared to their mold-casted counterparts. This work demonstrates the advantages of 3D printing over traditional fabrication methods, beyond the ability to rapidly fabricate complex architectures, to achieve improved processing dynamics for fabricating CNT-polymer nanocomposites with better structural and functional properties.