Reactive multilayer systems represent an innovative approach for potential usage in chip joining applications. As there are several factors governing the energy release rate and the stored chemical energy, the impact of the morphology and the microstructure on the reaction behavior is of great interest. In the current work, 3D reactive microstructures with nanoscale Al/Ni multilayers were produced by alternating deposition of pure Ni and Al films onto nanostructured Si substrates by magnetron sputtering. In order to elucidate the influence of this 3D morphology on the phase transformation process, the microstructure and the morphology of this system were characterized and compared with a flat reactive multilayer system on a flat Si wafer. The characterization of both systems was carried out before and after a rapid thermal annealing treatment by using scanning and transmission electron microscopy of the cross sections, selected area diffraction analysis, and differential scanning calorimetry. The bent shape of multilayers caused by the complex topography of silicon needles of the nanostructured substrate was found to favor the atomic diffusion at the early stage of phase transformation and the formation of two intermetallic phases Al0.42Ni0.58 and AlNi3, unlike the flat multilayers that formed a single phase AlNi after reaction.