As well as adding shapes to the current MPSuperShape selection, it is possible to drop (ie. de-select) shapes from the selection.
Individual shapes can be de-selected by first selecting it in MapPoint (click on the shape with the left mouse button). MapPoint indicates the shape has been selected by drawing a small black square at each vertex of the shape:
Right click on the map to display the MPSuperShape popup menu. Select the Drop menu item. The de-selection will be indicated with MPSuperShape returning the shape to its original colors (yellow in this example):
All of the current MPSuperShape shape selection can be simultaneously de-selected, by selecting the Drop All menu item on the popup menu.