Nanocomposite multilayers were fabricated by reactive magnetron sputtering with modulation periods of approximately 6 nm. The structure of the (Ti,AI)N/Mo multilayers was studied by X-ray diffraction (XRD), both in the low and high angle regions, while the interface morphology was probed by high-resolution transmission electron microscopy (HRTEM). Particular attention has been directed to the evolution of the roughness with the bias voltage. It was shown that with a bias voltage of -100 V these structures were prepared with relatively flat and smooth interfaces, albeit a certain level of intermixing that can have an interdiffusion width of approximately 0.6 nit in the roughest samples. Furthermore, the reduction in grain size and change in direction of preferential growth as bias increases is clearly visible from the selected area diffraction (SAD) patterns in HRTEM experiments. The high-angle XRD scans confirmed the reduction in grain size for the higher bias voltages, while from the simulation of the low-angle scans the grain roughness was estimated. A correlation between the evolution of roughness and nanohardness is also given, featuring the smoothest films hardness values as high as 51 GPa.