We have investigated the correlation between morphology and magnetic anisotropy in nanostructured Co films on Cu(001). The formation of nanoscale ripples by ion erosion is found to deeply affect the magnetic properties of the Co film. A surface-type uniaxial magnetic anisotropy with easy axis parallel to the ripples is observed. The origin of the magnetic anisotropy has been identified with the modification of thermodynamic-step distribution induced by ripple formation. At higher ion doses, when Co ripples detach and crystalline nanowires form, a strong enhancement of the magnetic anisotropy due to magnetostatic contributions is observed.