This command is accessed by Right-Clicking on a Map Layer. It creates a Sample Area for each enclosed polygon. Nested polygons become holes and islands. The pictures below illustrate the process.
Before:
Right-Click on Water Features and select Create Sample Areas for all Polygons, then select a color for the new Sample Areas using the color dialog:
The new Sample Areas will be created and named after the Map Layer:
If the process is repeated and a different color is selected (green in this case), the holes will be filled in with new Sample Areas: