The oxygen and silicon ions have been obtained respectively from pulsed energetic dense oxygen plasma and silane plasma generated by electrodeless discharge. The oxygen ions have been injected into superconducting Nb films, and the Si ions into superconducting YBCO films in order to investigate the variation of their superconductivity with the ions injected into them. Auger profile data show that the injection depths range from 20 to 40nm in the films,depending on the injection condition and film material. The resistance-temperature relations (R-T curves) indicate that the superconductivity remains unchanged in the photoresist-masked part of the film, but is significantly changed in the exposed part. The evenness of the film surface remains unchanged after injection. This technique may serve as an alteative to the planar inhibiting fabrication technique in the fabrication of the multi-layer structure of superconducting films, and also possibly to the conventional plasma source ion implantation technique in material surface processing.