A method and apparatus for processing data by a pipeline of a virtual multiple instance extended finite state machine (VMI EFSM). An input token is selected to enter the pipeline. The input token includes a reference to an EFSM instance, an extended command, and an operation code. The EFSM instance requires the resource to be available to generate an output token from the input token. In response to receiving an indication that the resource is unavailable, the input token is sent to a wait room or an initiative token containing the reference and the operation code is sent to a wait queue, and the output token is not generated. Without stalling and restarting the pipeline, another input token is processed in the pipeline while the resource is unavailable and while the input token is in the wait room or the initiative token is in the wait queue.