How about using a boolean node? Not sure what you need to do but in this case, I added some edge loops, inset the tops and then subdivided, before boolean (subtract).
For a flat (or oddly positioned like your second example) plane and a circular hole, you can select the primitives you want out of the way, delete them, then drop a polydraw, hold shift and drag-select the points on the edge of the hole, then press shift+C to create a circle.
if you have the geometry, then click on a square group of polygons, select MOVE then right click and choose make circle, delete resulting polygons, then drop a subdivide node.
bobc4d if you have the geometry, then click on a square group of polygons, select MOVE then right click and choose make circle, delete resulting polygons, then drop a subdivide node.
Thank you very much for your help - I finally I think the solution over selection -move-tool- make curve is working, on the tube example I used topobuild to bring back the curvature of the tube. Is there any other solution?