Benzaldimine monolayer was exposed to soft X-rays, and the involved chemical transformation was investigated using X-ray photoelectron spectra and near-edge X-ray absorption fine structure spectroscopy. The spectroscopy indicated that irradiation of soft X-ray (550 eV)-induced selective transformation of the imine group into a nonhydrolyzable one, i.e., the amine group. Utilizing the selective chemical transformation of the imine group with the soft X-ray irradiation, we were able to generate a micropattern. AFM images showed that the patterning with alternating surface topology was effective. The patterned monolayer was further modified with biotin and Cy3-tagged Streptavidin sequentially. Fluorescence images showed that the above molecules were selectively immobilized onto the amine-terminated region of the patterned surface. The current system is found to be more efficient than the predecessor, 4-nitrobenzaldimine monolayer.