The damage to the organic layer of aluminum (III) bis(2-methyl-8-quninolinato)-4-phenylphenolate (BAlq) film was investigated on the basis of the change in photoluminescence (PL) intensity. To suppress the bombardment of the substrate with high-energy particles such as γ-electrons and negative oxygen ions, we used a facing-target sputtering (FTS) system. A marked reduction, however, of the PL intensity of the organic layer was still observed upon the deposition of an indium tin oxide (ITO) film on the organic film. To reduce this reduction, we proposed the insertion of a sector-shaped metal shield near the target electrode, and we showed its effectiveness in reducing the damage. This reduction of the damage is thought to be caused by the elimination of γ-electrons incident to the organic film surface escaping from the target area near the substrate side. We confirmed that high-energy electron bombardment leads to a significant reduction of PL intensity of the organic layer. This indicates that high-energy electrons incident to the organic film surface play a key role in the damage of the organic layer during the sputtering process.