In both case, before exporting data into Matlab, you will need to interpolate the FDTD result into a uniform sampling mesh. This is because by default FDTD uses non-uniform mesh whereas matlab uses uniform mesh. Otherwise the image or plot in Matlab is distorted.
Please note that, interpolation with finer sampling does not improve the accuracy. in fact it has interpolation errors. The result accuracy is determined by FDTD simulation.