Reference an old closed ticket: http://feedback.arma3.com/view.php?id=10615

For those who doubt if it is at all possible:

https://vimeo.com/4824768 (ArmA)
https://www.youtube.com/watch?v=9QVf4eTZfCg (ArmA2)
https://www.youtube.com/watch?v=zVIvBDgcJn8 (ArmA2)
https://www.youtube.com/watch?v=ZGQ18q2AhZg (ArmA3)

Reality: The process of flattening terrain is probably incredibly resource intensive. The resource being information passed to server and clients in order to make this multiplayer friendly. How would the editor even know to put the objects on the newly flattened ground and not the old ground? How would the server and clients know to do the same thing?

I can understand how some of you have haughty attitudes regarding this. It might be so impractical that it isn't even worth thinking about anymore. Lucky for you, I am an idiot.

Daring to dream (the world is full of dreamers):
Regarding the issue of flattening parts of maps, it would be nice if there was a way for an island creator to define a "Filler Texture" (or multiple ones) in which the Mission maker/Base creator/Town creator/etc could use in the editor to add to the terrain.

I think subtracting from the terrain would be far more complex than adding, but maybe if you can do one you can do the other?

From there maybe a separate .sqf file is generated and can be added to the mission's init.sqf. Maybe this method would still require you to use setPos and setVectorUp commands however since I am still in my dreamy land I will say the objects will magically know to snap to the newly "flattened" terrain.

To you naysayers: https://www.youtube.com/v/Ib-VMe8etNE?start=18&end=60

There is more than one way to skin a cat.