Accurate modeling of diffusive transport of nanoparticles across nanopores is a particularly challenging problem. The reason is that for such narrow pores the large surface-to-volume ratio amplifies the relevance of the nanoscopic details and of the effective interactions at the interface with pore walls. Close to the pore wall, there is no clear separation between the length scales associated with molecular interactions, layering of the solvent at the interface with the pore and the particle size. Therefore, the standard hydrodynamic arguments may not apply and alternative solutions to determining average transport coefficients need to be developed. We here address this problem by offering a multiscale ansatz that uses effective potentials determined from molecular dynamics simulations to parametrise a four state stochastic model for the positional configuration of the particle in the pore. This is in turn combined with diffusivities in the centre of the pore and at the pore wall to calculate the average diffusion constant. We apply this model to the diffusion of fullerenes in a toluene filled slit nanopore and calculate the mean diffusion coefficient as a function of the pore size. We show that the accuracy of our model is affected by the partial slip of the toluene on the pore wall.