A scanning measurement system includes independently driven, self-aligning, dual-sided heads. The system is configured to perform a method that includes receiving information associated with a discrepancy in a desired cross direction alignment of a first sensor head and a second sensor head that are disposed on opposite sides of a web of material and that are configured to move in a cross direction relative to the web. The method also includes adjusting a velocity of at least one of the sensor heads based on the received information to improve the cross direction alignment of the first sensor head and the second sensor head.