We propose a scheme of overlay alignment for plasmonic lithography using a scanning contact probe. Using two resonances of a ridge aperture in a metal film, we introduce the aperture's multifunctional characteristics for patterning and alignment at different wavelengths. To verify this idea, we measure an image of an alignment mark using a scanning ridge aperture and determine the reference point for the alignment. We then analyze the uncertainty of the alignment method with respect to the image data noise and compare the numerical results with the experimental results. The uncertainty of the overlay alignment method is shown to be less than approximately 2 nm.