First, select an area about 2 blocks bigger than your structure. The command will - in very basic terms - place Natural Floor blocks below base blocks, and Negative Space blocks where it believes the structure doesn't extend to.
/#natural smart Edit
Calls floor and space at once.
/#natural space Edit
This command analyzes the selection, looking for air that is not supposed to be part of the structure and replacing it with negative space. This will make the structure integrate well with nearby constructs and terrain.
/#natural floor Edit
This command analyzes the selection looking to find the floor and adding natural floor blocks below it, to make it integrate into the terrain well.