Surfacing before 3D roughing

I have a piece of stock that is 18mm height and i want to mill out a 3D object that is only 5.5mm heigh out of the bottom of the stock. Is it possible to do a pocket surfacing path before i run the 3D rough pass? My surfacing tool would save a lot time to get down to the level i need cut at but every time i run the pocket path first, the 3D roughing pass still tries to cut out all of the same material starting at 18mm. Is there a setting or trick i can do to avoid running 3D roughing on the whole height?

in this screenshot you can see the 3d roughing op trying to start at the top of the stock, even though it has been removed by a prior pocket path.

Not in one file.

You would run the pocket in one file, then define the new stock thickness in the 3D file.

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