Deposition of 3,4,9,10-perylene-tetracarboxylic-dianhydride on iron island arrays on Au(111) results in the formation of new nanostructures. By controlling the amount of iron deposited on the gold surface, two kinds of aggregates are obtained: molecular chains and organic nanodots (see figure). These nanostructures possess a different density of states from the two-dimensional self-assembled molecular layer.