The technologically important exchange coupling in antiferromagnetic/ferromagnetic bilayers is investigated for embedded nanostructures defined in a LaFeO(3)/La(0.7)Sr(0.3)MnO(3) bilayer. Exploiting the element specificity of soft X-ray spectromicroscopy, we selectively probe the magnetic order in the two layers. A transition from perpendicular to parallel spin alignment is observed for these nanostructures, dependent on size and crystalline orientation. The results show that shape-induced anisotropy in the antiferromagnet can override the interface exchange coupling in spin-flop coupled nanostructures.