Self-organized patterning of supported nanoclusters by virtue of low cost and readiness for mass production is considered as one of the most promising methods; however, this approach is challenging, since the capability of controlling the patterns relies on a suitable combination of clusters and templates. In this paper we demonstrate that Co nanoclusters grown from vapour deposition over Al 2 O 3 thin films on NiAl(100) substrate make a perfect combination for self-organized patterning. Uniform and sizeable Co nanoclusters are formed only on crystalline Al 2 O 3 films and they are highly aligned by protrusion structures of the crystalline Al 2 O 3 . Through simple thermal treatments we can pattern the crystalline Al 2 O 3 films and consequently the grown Co nanoclusters. The patterns are robust as they are sustained even when the Co nanoclusters are flashed to 750 K, exposed to atmosphere or the coverage is increased to coalescence. Moreover, the patterns can be further refined by using STM tips. The results imply potential applications in both fundamental and applied researches for electronic and magnetic nanodevices as well as catalysis.