To remove the given com.nomagic.magicdraw.uml.symbols.PresentationElement from the diagram, use the method com.nomagic.magicdraw.openapi.uml.PresentationElementsManager.deletePresentationElement(PresentationElement):
PresentationElement element = ...;
SessionManager.getInstance().createSession("Test");
PresentationElementsManager.getInstance().removePresentationElement(element);
SessionManager.getInstance().closeSession();
All related presentation elements with all children and connected paths will be removed too.