If you set the origin at the top of the stock, then set up the file so that the parts of the model are within the thickness of the actual stock, and set up the toolpaths so that they never cut more deeply than the actual stock this should work — the only thing which would be lost would be some detail in the 3D preview.
That said, it should work to import the model at the original too-high thickness, check in the Design view the highest extent, then draw a rectangle the size of the entire working area and subtract that as a flat surface from everywhere to reduce the height consistently — I believe that is shown/discussed in: