Additive manufacturing (AM) is a class of manufacturing processes where material is deposited in a layer-by-layer fashion to fabricate a three-dimensional part directly from a computer-aided design model. With a current market share of 44%, thermoplastic-based additive manufacturing such as fused deposition modeling (FDM) is a prevailing technology. A key challenge for AM parts (especially for parts made by FDM) in engineering applications is the weak inter-layer adhesion. The lack of bonding between filaments usually results in delamination and mechanical failure. To address this challenge, this study embedded carbon nanotubes into acrylonitrile butadiene styrene (ABS) thermoplastics via a filament extrusion process. The vigorous response of carbon nanotubes to microwave irradiation, leading to the release of a large amount of heat, is used to melt the ABS thermoplastic matrix adjacent to carbon nanotubes within a very short time period. This treatment is found to enhance the inter-layer adhesion without bulk heating to deform the 3D printed parts. Tensile and flexural tests were performed to evaluation the effects of microwave irradiation on mechanical properties of the specimens made by FDM. Scanning electron microscopic (SEM) images were taken to characterize the fracture surfaces of tensile test specimens. The actual carbon nanotube contents in the filaments were measured by conducting thermogravimetric analysis (TGA). The effects of microwave irradiation on the electrical resistivity of the filament were also reported.