According to one embodiment, a stage apparatus includes a height control unit includes height control elements each which is drove in an upward/downward direction independently, a measuring unit which divides an upper surface of the substrate into areas, and measures a height of each of the areas. The control unit is configured to set the height of each of the areas independently by controlling a height of each of the height control elements based on a data value, determine using the measuring unit whether the height of each of the areas in the upper surface of the substrate is in a allowable range, and set the height of the area out of the allowable range again by the height control elements.