Methods and systems for optimizing measurement system parameter settings of an x-ray based metrology system are presented. X-ray based metrology systems employing an optimized set of measurement system parameters are used to measure structural, material, and process characteristics associated with different semiconductor fabrication processes with greater precision and accuracy. In one aspect, a set of values of one or more machine parameters that specify a measurement scenario is refined based at least in part on a sensitivity of measurement data to a previous set of values of the one or more machine parameters. The refinement of the values of the machine parameters is performed to maximize precision, maximize accuracy, minimize correlation between parameters of interest, or any combination thereof. Refinement of the machine parameter values that specify a measurement scenario can be used to optimize the measurement recipe to reduce measurement time and increase measurement precision and accuracy.