When a substrate stage is located in a first area, a first measurement device measures the same portion of the substrate at the plural measurement points both before and after the stage is horizontally driven. A controller calculates a first difference of the stage in the vertical direction in the first area accompanying driving of the stage horizontally, based on a first measurement result, calculates a value representing a surface shape of the substrate by subtracting the first difference from the first measurement result, calculates a second difference of the stage in the vertical direction in the second area accompanying driving of the stage horizontally by subtracting the value from a value representing a vertical position of the substrate when the stage is located in the second area, and controls a vertical position of the stage in the second area based on the second difference.