The phenomenon of shear-induced alignment in polycrystalline bilayer systems is analyzed using Brownian dynamics simulations. We show that the alignment process can be explained in terms of a local grain boundary migration mechanism. Both microscopic and continuum models are constructed that predict the boundary migration velocity as a function of local structure and shear stress. In the continuum picture, shear-induced potential energy gradients act as the driving force for migration, and the grain boundary mobility is sensitive to the degree of misorientation between the grains.