To permit correcting the amount of positional displacement caused by the vertical movement of a movable stage by instrumentation, by a method wherein the reference member, which becomes the reference in the first direction of a stage is fixed to the stage located on the position lower than the upper surface of the stage.

A reference mark 35, to be used for alignment in X and Y directions of a mask and a photosensitive substrate 26, is fixed to a Z-stage 24 located lower than the upper surface of a substrate holder 25. When an aligner is initiallized, the Z-stage 24 is moved up when the reference mark 35 is necesary, and the reference mark 35 is provided in the height of the reference surface of an alignment microscope. When the positional displacement amount Δt1 is generated in X and Y directions on the Z-stage 24, it is measured by an interferometer system using the displacement amount when vertical movement is Δt2. The Z-stage 24 is adjusted based on the above- mentioned displacement amount, and the coordinate position in X and Y directions of the reference mark on the focus surface of the microscope is corrected. As a result, the indeterminate microscopic positional displacement caused by the vertical movement of the Z-stage can be eliminated, and a highly precise alignment can be conducted.