A microwave-induced heating of CNT filled (or coated) polymer composites for enhancing inter-bead diffusive bonding of fused filament fabricated parts. The technique incorporates microwave absorbing nanomaterials (carbon nanotubes (CNTs)) onto the surface or throughout the volume of 3D printer polymer filament to increase the inter-bead bond strength following a post microwave irradiation treatment and/or in-situ focused microwave beam during printing. The overall strength of the final 3D printed part will be dramatically increased and the isotropic mechanical properties of fused filament part will approach or exceed conventionally manufactured counterparts.