Carbon nanotube (CNT) based polymeric composites exhibit high strength and thermal conductivity and can be electrically conductive at a low percolation threshold. CNT nanocomposites with polystyrene (PS) thermoplastic matrix were injection-molded and high shear stress in the flow direction enabled partial alignment of the CNTs. The samples with different CNT concentrations were prepared to study the effect of CNT concentration on the cutting behavior of the samples. Characterizations of CNT polymer composites were studied to relate different characteristics of materials such as thermal conductivity and mechanical properties to micromachining. Micro-end milling was performed to understand the material removal behavior of CNT nanocomposites. It was found that CNT alignment and concentrations influenced the cutting forces. The mechanistic micromilling force model was used to predict the cutting forces. The force model has been verified with the experimental milling forces. The machinability of the CNT nanocomposites was better than that of pure polymer due to the improved thermal conductivity and mechanical characteristics.