Terrain Holes/Set Empty

I've looked at a number of posts related to cutting holes into terrain
for underground .dif interiors, but I have not been able to get
things working as I need them too.

I'm making an interior .dif with 3 levels/stories. 2 above ground and one underground.
I have not enclosed the interiors with ceilings, because I want to have the option
of having an observer camera positioned high above for an omniscient point of view.
The "underground" floor is just one room. It is accessed by a cutout in the floor with
a staircase leading down. The size of this access hole is about 1x1 meter.
In my project, when I move the player to the location of the access point, I can see the
terrain, and of course can not move down the stairs into the below ground level.

From my research in the posts, I saw that using the Select Empty function in terrain editing mode would cut holes into the terrain, so I thought that I could just cut a hole
in the terrain where my access point is in the floor and my problem would be solved.

I was able to cut a really big hole, but not a small one. When I set the brush to
any size lower than 9x9, nothing happens. I tried to patch a large hole
with the Clear Empty option using a 1x1 brush, but wasn't able to get a small
hole that way either, it just filled in with a few clicks.

So what I'd like to find out is how, if it is possible to cut small
holes into the terrain.

BTW: I also tried capping the access point with a portal that extended above and
below floor where the opening is, but that didn't work either
(showTerrainInside is set to "0")

Thanks in advance for help with this.

PS - I think that this is my first post here :)