For devices of bonded silicon and glass structures fabricated by deep reactive ion etching (DRIE), it is important to avoid damage at the silicon sidewall and backside during through-wafer etching in order to ensure reliability of devices. The silicon damage caused by charge accumulation at the glass surface is inhibited by means of an electrically conducting layer patterned onto the glass and connected with the silicon. In this study, indium tin oxide films were applied in order to identify the positions of silicon damage in the structural layout without destruction of samples. From the results, we report that there exists silicon damage caused by charge accumulation at the silicon islands divided by DRIE and we present important rules for mask layout when utilizing this method.