A method and apparatus for positioning an end effector relative to a fuselage assembly. The end effector is positioned relative to an expected reference location for a reference point on the fuselage assembly using data from a first metrology system. After positioning the end effector relative to the expected reference location, an actual reference location for the reference point on the fuselage assembly is identified using data from a second metrology system. The end effector is positioned at an operation location based on the actual reference location identified.