Use the IBM® Integration API when developing message flow applications to remove a node from a message flow.
File msgFlow = new File("main.msgflow");
MessageFlow mf1 = FlowRendererMSGFLOW.read(msgFlow);
Node mqinNode = mf1.getNodeByName("My Input Node");
mf1.removeNode(mqinNode);
MessageFlow mf1 = patternInstanceManager.getMessageFlow("MyFlowProject", "main.msgflow");
Node mqinNode = mf1.getNodeByName("My Input Node");
mf1.removeNode(mqinNode);