@gaieus said:
You can still copy an array of the bottom (bigger) face of the prism and then intersect the shape with the copied faces. In the attached file, edit the group, select all inside and intersect with model. This way only the faces will get intersected but no inner faces created. If you need those inner faces, too, explode the group, select all, intersect with model or selected and then start removing access geometry of the multiple octagons copied.
Thanks Gai it worked a treat and was what I was after. Will post the model when it is done