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We investigate the surface structure and composition ofa YBa2Cu3Oy (YBCO) thin film modified by CF4 plasma fluorination. In addition to the absorption of hydrocarbons, chemical reactions of the YBCO surface take place during CF4 plasma treatment. Various x-ray photoelectron spectroscopic data are reported and discussed. The existence of a thin barrier is confirmed, which homogeneously covers the edge of the base YBCO film in our interface engineering Josephson junction. Measurements of Auger electron spectroscopic data and the resistance versus temperature indicate that the barrier is a controllable-insulating layer.