Use JSONObject recursively. Try something like this (I add some extra indentation so it can be readed easily, but on real projects better use functions instead):

JSONObject json = new JSONObject();
  JSONArray scene = new JSONArray();
    JSONObject node = new JSONObject();
    node.put("id", 0);
    node.put("calendar_event", "urlaub");
      JSONArray element = new JSONArray();
        JSONObject enode = new JSONObject();
        enode.put("anything", "");
      element.add(enode);
      //...
    node.put("element", element);
  scene.add(node);
json.put("scene", scene);
//...

Note like this you generate manually the JSONs, but there are other libraries that scan objects to generate jsons. Depending on your needs, it could be easer, but remember that making so you are going to overhead everything because you are going to need to hold in memory two copies of the same tree. Also dealing with hierarchical structures maybe a problem using plain java objects.