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Arrays of amorphous and polycrystalline CoxSi1-x nanowires have been prepared by electron beam lithography and a lift-off technique. The angular dependence of the magnetooptical transverse Kerr-effect hysteresis loops for both kind of samples has been compared in order to analyze the interplay between material microstructure and element shape at the submicrometric scale. The overall magnetic properties of the Co-Si nanowires are found to be dominated by patterning induced shape anisotropy, with the presence of coherent rotations in the magnetization reversal process in a wide angular range around the hard axis direction. It is found that the more homogenous microstructure of the amorphous samples results in a softer magnetic behavior and on a much better definition of the wires uniaxial anisotropy.