A method for aligning existing layers formed prior to a new layer and the new layer in forming the new layer on a wafer 4, wherein a microscope 6 as a first measurement condition and a microscope 7 as a second measurement condition are used, and marks 4a and 4b formed in each of said existing layers are measured by switching the first and second conditions, and said existing layers and said new layer are aligned based on measurement of mark position of each of said existing layers, and the microscope 7 has a plurality of measurement conditions as optical characteristics, and the measurement conditions are switched.