In the last years, well-ordered nanoclusters attract a lot of attention, because they are effectively used to enhance the catalytic capability and Curie temperature for ferromagnetism. However, in the conventional case, the nucleation sites will form 2-dimensional islands and then grow into films with increasing coverage. This kind of 2-D islands restricts the function for the further applications. Thus, in this report, we controlled the growth of 3-D Fe nanoclusters by the method of buffer layer assisted growth (BLAG) on Au(111) herringbone reconstruction structure. The method of BLAG was used to control the Fe nanoclusters size from 2 to 6 nm by the amount of Xe buffer layer and Fe deposition. In addition, the Fe nanodots are confined and arranged at the turning points of the Au(111) herringbone by Fe seeds before the BLAG method. They can be used as the nucleation sites to assemble the well-order nanoclusters by BLAG. From the result, the size controlled 3-D Fe nanoclusters self-assemble at special point. The method of ¡§BLAG on nano-patterned template¡¨ will be very helpful to prepare various 3-D nanoclusters with regular spatial arrangement and to control size of them.