A method and system are disclosed enabling configuration of a control system for an electrosurgical generator system for creating new surgical applications without changing the underlying software system. The programmable electrosurgical generator system has an RF output stage for outputting at least one RF operating waveform for performing an electrosurgical procedure. The programmable electrosurgical generator system includes an inner loop system to change at least one parameter of the at least one RF operating waveform an outer loop system to provide at least one operating command to the inner loop system and a configuration control system that modifies at least one of the inner and outer loop systems based on received data from a sensor module.
