Nanobeam electron diffraction can probe local structural properties of complex crystalline materials including phase, orientation, tilt, strain, and polarization. Ideally, each diffraction pattern from a projected area of a few unit cells would produce a clear Bragg diffraction pattern, where the reciprocal lattice vectors can be measured from the spacing of the diffracted spots, and the spot intensities are equal to the square of the structure factor amplitudes. However, many samples are too thick for this simple interpretation of their diffraction patterns, as multiple scattering of the electron beam can produce a highly nonlinear relationship between the spot intensities and the underlying structure. Here, we develop a stacked Bloch wave method to model the diffracted intensities from thick samples with structure that varies along the electron beam. Our method reduces the large parameter space of electron scattering to just a few structural variables per probe position, making it fast enough to apply to very large fields of view. We apply our method to SrTiO3/PbTiO3/SrTiO3 multilayer samples, and successfully disentangle specimen tilt from the mean polarization of the PbTiO3 layers. We elucidate the structure of complex vortex topologies in the PbTiO3 layers, demonstrating the promise of our method to extract material properties from thick samples.