This work presents a theoretical study of the translocation routes of nanoparticles through polymer-brush modified nanopores. The calculations were performed with a molecular theory that explicitly accounts for the shape, size, conformations and interactions of all molecular species in the system. This work reports molecular-theory calculations allowing inhomogeneities in the three spatial dimensions, which allows us to study for the first time off-axis translocation routes, i.e. routes that do not coincide with the axis of the pore. Free-energy landscapes within the pore were obtained for particles of different sizes and affinity for the polymer brush. The minimum free-energy paths on these landscapes determine the translocation routes. Decreasing the size of the particle or increasing its affinity for the polymer, shifts the translocation route from the central axis of the pore towards its walls. Interestingly, for a given polymer-particle affinity, there exists an intermediate particle size that results in the most flat potential of mean force for translocation, therefore, that will optimize the rate of translocation.