The effect of layer structure perturbations on antiferromagnetic coupling in Fe-Cr-Fe trilayer systems is investigated. By varying the sputtering pressure, the layer structure of Fe-Cr-Fe trilayers is systematically altered, as indicated by changes in the low angle superlattice spectra of multilayers fabricated under identical conditions. The effect of topographic roughness is investigated by fabricating identical trilayers on Cr buffer layers of different thickness. Scanning tunneling microscopy is used to measure surface roughness. In each case the saturation field is measured as a function of Cr interlayer thickness by means of tapered Cr interlayer structures in which the thickness of the spacer varies linearly from 0 to 28 Å upon a single substrate. Antiferromagnetic coupling is measured locally by means of the magneto-optic Kerr effect. Results show that although the coupling is diminished by structural perturbations, it is a remarkably robust effect which persists even in instances of poor layer structure.