We compare 3-D upper mantle anisotropic structures beneath the North American continent obtained using standard and improved crustal corrections in the framework of Non-linear Asymptotic Coupling Theory (NACT) applied to long period three component fundamental and higher mode surface waveform data. Our improved approach to correct for crustal structure in high-resolution regional waveform tomographic models goes beyond the linear perturbation approximation, and is therefore more accurate in accounting for large variations in Moho topography within short distances as observed, for instance, at ocean-continent margins. This improved methodology decomposes the shallow-layer correction into a linear and non-linear part and makes use of 1-D sensitivity kernels defined according to local tectonic structure, both for the forward computation and for the computation of sensitivity kernels for inversion. The comparison of the 3-D upper mantle anisotropic structures derived using the standard and improved crustal correction approaches shows that the model norm is not strongly affected. However, significant variations are observed in the retrieved 3-D perturbations. The largest differences in the velocity models are present below 250 km depth and not in the uppermost mantle, as would be expected. We suggest that inaccurate crustal corrections preferentially map into the least constrained part of the model and therefore accurate corrections for shallow-layer structure are essential to improve our knowledge of parts of the upper mantle where our data have the smallest sensitivity.