We present a synchrotron-based X-ray scattering technique which allows disentangling magnetic properties of heterogeneous systems with nanopatterned surfaces. This technique combines the nmrange spatial resolution of surface morphology features provided by Grazing Incidence Small Angle X-ray Scattering and the high sensitivity of Nuclear Resonant Scattering to magnetic order. A single experiment thus allows attributing magnetic properties to structural features of the sample; chemical and structural properties may be correlated analogously. We demonstrate how this technique shows the correlation between structural growth and evolution of magnetic properties for the case of a remarkable magnetization reversal in a structurally and magnetically nanopatterned sample system.