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Topography (transparent layer) and circle in XY and XZ views

To trim the terrain we will extrude cylindrical surfaces and use them for intersection

Utilities->Copy...

A translation of 3000 m in z, extruding surfaces

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Copy with extrusion 

And calculate numerically the intersection of surfaces with:

Geometry->Edit->Intersection->Surfaces

Try to select the minimum surfaces possible, because will find the intersection of the selected surfaces all against all, and it could be very expensive in time.

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Selection of surfaces to be intersected