The manipulated nucleation of Fe on hexagonal close-packed (hcp) and face centered cubic (fcc) areas of an Au(111) herringbone surface was demonstrated with the combined growth methods of Xe buffer layer, seed effect and low temperature deposition. Besides the herringbone kinks, bi-layer stacking at fcc gaps was observed. This preference resulted in various nucleation patterns, such as zigzag stripes and doublet islands, by properly choosing the growth condition. The idea of nucleation control through combined growth methods can be applied in other nanopatterned templates for the fabrication of self-assembled nanostructures.