You can delete objects using the Delete method.
Dim MyModel, obj, sym, idx
set MyModel = CreateModel(PdCDM.Cls_Model)
MyModel.SetNameAndCode "MyCDM" , "MyCDM"
'Create entities
For idx = 1 to 12
Set obj=MyModel.Entities.CreateNew()
obj.SetNameAndCode "E" & idx, "E" & idx
Set sym=ActiveDiagram.AttachObject (obj)
Next
'Create relationships
For idx = 2 to 11
Set obj=MyModel.Relationships.CreateNew()
obj.SetNameAndCode "R" & idx-1, "R" & idx-1
Set obj.Object1 = MyModel.FindChildByName("E" & (idx-1),cls_entity)
Set obj.Object2 = MyModel.FindChildByName("E" & (idx+1),cls_entity)
Set sym=ActiveDiagram.AttachLinkObject (obj)
Next
ActiveDiagram.AutoLayoutWithOptions(2)
'Delete objects
MyModel.FindChildByName("E5",cls_entity).Delete
MyModel.FindChildByName("R8",cls_relationship).Delete