Macroscopic poly(ether ether ketone) (PEEK) and polypropylene (PP) nanocomposites containing vapour-grown carbon nanofibres (CNF) were produced using standard polymer processing. Tensile tests revealed a linear increase in composite stiffness with nanofibre content. A detailed DSC study verified that under standard processing conditions the degree of crystallinity and the crystalline structure of these semicrystalline thermoplastics were not affected by the nanofibres. Nevertheless, we provide evidence that the nanoscale filler can alter the polymer morphology under certain conditions, an effect which needs to be considered when evaluating nanocomposite properties. Given the absence of morphological changes in the standard nanocomposites we were able to calculate the intrinsic nanofibre modulus using short fibre theory; both distinctively different matrix systems show a similar effective nanofibre modulus.