There are layers in PW; untick all of those except for the element you want to remove, then select them all with the Vertex Selection Tool (don't use [CTRL] + A; this still selects even invisible layers), and delete them.
I'm not exactly sure where but there is a line in polyworks.ini that allows you to change the max. # of undos you can make (it's currently set to 10; a larger or lower # will eat up more RAM accordingly).
