Deleting a polyfill is similar to deleting a segment:
1) Using the Subselect tool, click on the polyfill. (If the Properties Palette is showing, it should switch to showing PolyFill Properties.)
NOTE: The PolyFill Tool is only for creating polyfills, not for selecting them.
2) Hit the Backspace or Delete key, or choose Edit > Delete.
That's it! If you made a mistake, you can always Undo (Edit > Undo Delete PolyFill).