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.