Ion beam irradiation has been shown to be an interesting tool for tailoring the magnetic properties of thin films and multilayers. The modified properties include magnetic anisotropy, interlayer exchange coupling, exchange bias, magnetic domain structure and magnetization reversal. In this work, new results are shown concerning the enhancement, by one order of magnitude, of the antiferromagnetic coupling strength in amorphous CoSi/Si multilayers by irradiating Si(100) substrates with 1 keV Ar(+) ions. The ion beam exposure induces an increase of the substrate roughness, from 0.07 to 0.88 nm, which enhances antiferromagnetic coupling in the magnetic multilayers grown on top. One possible mechanism governing this enhancement is discussed, related to the formation of magnetic/non-magnetic regions where dipolar interactions could stabilize the antiferromagnetic alignment. The presence of non-magnetic regions is suggested by the observed trend to superparamagnetism, and is expected since the Curie temperature of the amorphous CoSi alloy used is slightly above but very close to room temperature. Accordingly, small fluctuations in the local composition, leading to an enrichment of Si, would produce non-magnetic regions enabling dipolar interactions to take place. Furthermore, the ion beam induced increase of roughness makes surface diffusion of the atoms arriving at the sample difficult, favoring the formation of local non-magnetic inhomogeneities. Finally, the role of other possible mechanisms to enhance antiferromagnetic coupling is also briefly discussed.