Export Roof & Floor from geological units for Modflow

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Hi there! I'm trying to export roof and floor from each unit of my geological model, but these are highly dipping, and are also eroded by alluvium on top.
So when I try to export the mesh parts of my younger and older surface I get the lateral contact and part of the topography. What would be the easiest way to export roof and floor surfaces for Modflow?
TIA

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