cut out by hand using the split poly tool its really not that hard
draw on the surface so you have enough vert for the shape.
line uup the other object on the surface of what u r wanting to extract. use snap to point(vert) option and move into plae.
delete inner face
extrude in
dup -1 to mirror and join the vert

this technique works even if u want to cut out circles doesnt matter what shape u want