By anodizing an aluminum surface that has been patterned with different guiding lattices using a focused ion beam, the resulting anodic alumina nanochannel arrays exhibit different degree of order arrangement. Long-range order is achieved only when the guiding lattice is carefully matched to that of the self-organized hcp array formed locally in an unguided area. Lattice mismatch between the guiding and locally self-organized lattice leads to an order-disorder transition via the creation and annihilation of nanochannels. The driving force of the transition is attributed to the unbalance in the stress among the nanochannels. (C) 2004 American Institute of Physics.