To achieve the 2 nm overlay accuracy required for double patterning, we have introduced the NSR-S620D immersion scanner that employs an encoder metrology system. The key challenges for an encoder metrology system include its stability as well as the methods of calibration. The S620D has a hybrid metrology system consisting of encoders and interferometers, in XY and Z. The advantage of a hybrid metrology system is that we can continuously monitor the position of the stage using both encoders and interferometers for optimal positioning control, without any additional metrology requirements or throughput loss. To support this technology, the S620D has various encoder calibration functions that make and maintain the ideal grid, and control focus. In this paper we will introduce some of the encoder calibration functions based on the interferometer. We also provide the latest performance of the tool, with an emphasis on overlay and focus control, validating that the NSR-S620D delivers the necessary levels of accuracy and stability for the production phase of double patterning.