Michael,
If you are using our MapShapeLayer and MapShape API in MapSuite 5.x, you can see the example below where I add two MapShapes to the map by adding to the MapShapeLayer and then clear the collection of MapShapes from the MapShapeLayer. Also, I recommend that you read the descrption of the sample MapShapes of the Code Community. It gives a good background to understand the history of MapShapes in MapSuite wiki.thinkgeo.com/wiki/Map_Suite_De...#MapShapes
MapShape mapShape1 = new MapShape(new Feature(new PointShape(-90, 30)));
mapShape1.ZoomLevels.ZoomLevel01.DefaultPointStyle = PointStyles.Capital3;
mapShape1.ZoomLevels.ZoomLevel01.ApplyUntilZoomLevel = ApplyUntilZoomLevel.Level20;
MapShape mapShape2 = new MapShape(new Feature(new PointShape(-82, 36)));
mapShape2.ZoomLevels.ZoomLevel01.DefaultPointStyle = PointStyles.City2;
mapShape2.ZoomLevels.ZoomLevel01.ApplyUntilZoomLevel = ApplyUntilZoomLevel.Level20;
MapShapeLayer mapShapeLayer = new MapShapeLayer();
mapShapeLayer.MapShapes.Add("1",mapShape1);
mapShapeLayer.MapShapes.Add("2", mapShape2);
LayerOverlay mapShapeLayerOverlay = new LayerOverlay();
mapShapeLayerOverlay.Layers.Add(mapShapeLayer);
Map1.Overlays.Add(mapShapeLayerOverlay);
//To clear all the MapShapes
mapShapeLayer.MapShapes.Clear();