A method of manufacturing an array of nanoclusters and a substrate with an ordered array of nanoclusters. In a preferred embodiment of the invention, nanoclusters may be fabricated by depositing adatoms upon a surface containing an array of etched nanoscale wells, wherein the etched nanoscale wells are produced by etching a surface patterned by a mask containing a regular array of nanoscale pores. More preferably, nanoclusters may be fabricated by depositing adatoms upon a surface containing an array of etched nanoscale wells; wherein, the etched nanoscale wells are produced by low damage etching of a surface patterned by a crystalline mask of biological origin containing a regular array of nanoscale pores. A still further embodiment of the invention is a substrate including an ordered array of nanoclusters.