This work investigates the primary sinusoidal bifurcation wrinkling response of single-and multi-layered magne-torheological elastomer (MRE) film-substrate systems subjected to combined transverse applied magnetic fields and in-plane biaxial pre-compression. A recently proposed continuum model that includes the volume fraction of soft-magnetic particles is employed to analyze the effect of the magnetic properties upon the bifurcation response of the system. The analysis is built in a highly versatile manner using a finite-element discretization approach along the direction of the applied magnetic field and Fourier expansions along the infinite in-plane layer directions. This allows for a seamless investigation of various multi-layered structures. First, we analyze the effect of biaxial pre-compression upon the critical magnetic field for a film-substrate system and for various mechanical stiffness ratios. We observe a kink in the critical magnetic curves and a reflection in the corresponding wave numbers as they cross the equi-biaxial pre-compression regime. Subsequently, we consider a MRE film bonded to a MRE substrate and study the effect of the particle volume fraction ratios in those two parts. As a result, we obtain sharp pattern transitions, i.e., long to short wavelengths changes with only minor perturbations of the applied pre-compression. The presence of a magnetic sub-strate changes qualitatively and quantitatively the bifurcation response of the film/substrate system. Finally, we carry out a data-mining exercise to minimize the critical magnetic field at bifurcation by using three different topologies, i.e., a monolayer, a bilayer and a sandwich film. We find that the topologies resembling closely the monolayer one lead to the lowest critical magnetic fields for a given biaxial pre-compression.