Exclusive evidence of magnetic structure modification has been revealed by depth-sensitive polarized neutron scattering measurements in an antiferromagnetically coupled specimen upon swift heavy ion irradiation. The effects are independent of any structural modifications within the system (such as intermixing or roughness) that may normally have contributed to the changes in magnetic structure as well. The modifications include (a) the loss of uniaxial anisotropy, (b) changes in the variation of the mean magnetization angle and (c) changes in the variation of the lateral and longitudinal magnetic correlation lengths. We explain the changes within the thermal spike model. The possibility of controlling local magnetization can be foreseen from these results, which can be done even without damaging the structure.