Annealing of nanoscale Ni/C multilayers and C/Ni/C trilayers at temperatures above about 670 K leads to the formation of separated Ni particles embedded in carbon. The agglomeration of the Ni layers starts by the formation of holes in the Ni layer and proceeds by hole growth and hole coalescence, Different thermodynamic driving forces and kinetic processes which can affect the observed agglomeration are discussed. The formation of holes by thermal grooving of Ni grain boundaries is analyzed quantitatively.