The present invention features a laser based system configured with a noise detection unit. The system includes a mode-locked oscillator. A noise detection unit includes at least one optical detector that monitors optical pulses generated by the mode-locked oscillator and produces an electrical signal in response to the optical pulses. The noise detection unit includes a first filter to transmit signal power over a signal bandwidth which includes the mode-locked laser repetition frequency, frep. The noise detection unit may include one or more filters to transmit power over a noise bandwidth that substantially excludes repetition frequency, frep. Non-linear signal processing equipment is utilized to generate one or more signals representative of the power in the signal bandwidth relative to the power in the noise bandwidth. The system includes a controller operable to generate a signal for controlling the laser based system based on the relative power.