To optimize the current-voltage characteristics of Nb/AlOx-Al/Nb Josephson tunnel junctions, a uniform and well defined insulating barrier (AlOx) is required so that no leakage current occurs between the upper and lower Nb electrodes. We investigated the dependence of the surface morphology of dc magnetron-sputtered Nb thin films on deposition parameters using atomic force microscopy (AFM), the cross-sectional microstructure of the Nb/AlOx-Al/Nb trilayers using transmission electron microscopy (TEM), and anodization profiling. The surface roughness of the base Nb layer was found to affect the AlOx-Al layer and thus the quality of Nb/AlOx-Al/Nb trilayer. Diffusion of Al at the Al/Nb interface increases with increasing roughness of the base Nb layer, which increases the minimum Al thickness required to cover base-Nb. The importance of sufficient sample-cooling during the trilayer deposition was also confirmed by the TEM study and anodization profiling.