X-ray metrology for control of polishing

A polishing apparatus, comprising:

• a first polishing station;
• a second polishing station;
• a transfer station;
• a carrier head configured to receive a substrate and transport the substrate in sequence to the first polishing statin, the second polishing station and the transfer station;
• an x-ray monitoring system having a probe located in the second polishing station, between the first polishing station and the second position station, or between the second polishing station and the transfer station;
• and
• a controller configured to receive a first measurement of a first amount of metal on a substrate made after a first metal layer is deposited on the substrate and before a second metal layer is deposited on the substrate, receive a second measurement of a second amount of metal on the substrate from the x-ray monitoring system after the second metal layer is deposited on the substrate;
• compare the first measurement to the second measurement to determine a difference, and adjust a polishing endpoint or a polishing parameter of the polishing apparatus based on the difference.