The Problem

I have a cavernous map and I wish to have the ground level naturallized. I have it within my cuboid selection but when I go to //naturalize it only will cover areas that are exposed to the sky which is like only 5% of my map. And it leaves patchy blotches which look bad.

As It was explained to me this effect is occurring because World Edit starts from the highest Y and works downward. But it won't go below the first one it encounters. I need this effect to work even if there is exposed stone underneath more stone like the ground floor of a cave. This can make caves look far more lush.

A Solution

Redesign the logic so that it will naturalize any stone that has 1 air block above it and only above it (not sides or underside), and is within your cuboid selection. This way it will work for caves and give caves a grassy / dirt layers.

Maybe add it as an option with -all so //naturalize -all so it will not use logic to only do stone exposed to the sky downwards but also stone and the 3 blocks below it with dirt even in caves if the cave stone is selected.

Alternatives

Added by @octylFractal: Move your selection so the top is beneath the blocks. This may not always be preferable, especially if you have many vertically varied areas to apply naturalize to that are all underground.

only will cover areas that are exposed to the sky

This is false, as I stated multiple times on Discord. It goes from the top of your selection, you are free to move your selection to cover underground areas.