We investigated the effect of flow field and deformation rate on the nanotube alignment and on the properties of PC/multiwalled carbon nanotube nanocomposites. Samples of various MWCNT loadings were prepared by diluting a commercial masterbatch containing 15 wt% nanotubes using optimized melt mixing conditions. Different processing conditions were then used to systematically change the degree of nanotube alignment, from random orientation to highly aligned. Morphological studies and Raman spectroscopy analysis revealed that the nanotubes are preferentially aligned in the flow direction, particularly at large injection or compression rates. Rheological measurements corresponding to high shear rate conditions showed drastic changes in the viscoelastic behavior. The complex viscosity significantly decreased and percolation threshold notably rose. High degrees of nanotube alignment also resulted in a significant increase in the electrical percolation threshold. The mechanical properties of the nanocomposites for different nanotube loadings were also shown to depend on the processing conditions, and somehow improved when the material was processed at higher rates. Finally, we used a power-law type equation to correlate the percolation behavior and the nanotube alignment. The estimated percolation threshold and the power index, q, significantly increase with the degree of nanotube alignment as determined by Raman analysis.