We have correlated a detailed quantitative structural analysis by x-ray diffraction, transmission electron microscopy, and high spatial resolution electron energy-loss spectroscopy imaging, with the magnetization and anisotropic magnetotransport properties in sputtered Fe/Cr superlattices. To accomplish this, we developed a technique for magnetotransport measurements in metallic superlattices with the current perpendicular to the plane of the layers (CPP). Using microfabrication techniques, we have fabricated microstructured Fe/Cr pillars embedded in ${\mathrm{SiO}}_{2}$ and interconnected with Nb electrodes. Because of the uniform current distribution in the Nb electrodes and the minimization of the superlattice-electrode contact resistance, the method allows a simple and independent measurement of the superlattice resistance and giant magnetoresistance (GMR). Structural and magnetic characterization of $[\mathrm{Fe}\mathrm{}(3\mathrm{}\mathrm{n}\mathrm{m})/\mathrm{C}\mathrm{r}\mathrm{}(1.2\mathrm{}\mathrm{n}\mathrm{m}){]}_{N}$ superlattices (where N is the number of repetitions) indicate that the roughness is correlated and increases cumulatively through the superlattice stack with no significant change in the antiferromagnetic coupling. Both the current in-plane and CPP GMR increase with N as the roughness increases.