Another approach, inspired by the description as "like islands with the oceans gone":
Cover the world with a shallow ocean.
Build coral reefs.
Create an organism that builds up atolls just a bit higher than sea level.
Gradually raise the sea level so that the atolls get built up higher in response. (perhaps a one-time reaction to a wandering planet brings a cascade of ice comets to the inner planets, or an ice cap melts.)
After the ocean is deep enough, new reefs and atolls can't get started, but existing ones can keep getting taller as the oceans rise.
Remove the mechanism that adds water to the planet; in time the oceans will evaporate.
Leave just enough ocean in the deeper parts that there is a weather cycle bringing enough water to the pillars for life.
over time the former ocean bottoms will get their own ecosystem but the soil will be salty enough that it won't be a productive one.
you will need a mechanism for cycling biomass onto the pillar tops. Guano from deep flying birds should cover most of that.