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Etching the damage of a patterned media fabricated with an artificially assisted self-assembled mask is estimated. CoCrPt thin films were etched by ion milling into aligned dots with a diameter of 40 nm. The milling condition was optimized for reducing the etching damage. As a result, the damage to the crystal lattice and crystal orientation was estimated to be slight by transmission electron microscope (TEM) and scanning electron microscope (SEM) analyses. Though strong perpendicular anisotropy was induced by the patterning process, magnetic measurements and Landau-Lifshitz-Gilbert simulation revealed that the magnetic anisotropy energy was almost unchanged throughout this etching process. © 2004 American Institute of Physics.