The disintegration of Nb layers in Nb/Cu multilayers during heat treatments was investigated by means of X-ray diffraction (XRD), transmission electron microscopy (TEM), and X-ray microscopy (XRM). Spherically shaped Nb particles were observed after a heat treatment at 870 K for 3 h. The growth velocity of the Nb particles depends strongly on the initial interface roughness and the Nb layer thickness. The XRM investigations indicate a process of self-assembly, leading to a non-statistical distribution of the particles. Measurements of the superconducting properties of both annealed and non-annealed samples, confirm the microstructural observations.