This study shows the effects of deionized (DI) rinse and oxide HF wet etch processes on silicon substrate during a photolithography process. We found a fail at the wafer center after DI rinse step, called Si pits, during the fabrication of a complementary metal-oxide-semiconductor (CMOS) device. We tried to find out the mechanism of the Si pits by using the silicon wafer on CMOS fabrication and analyzing the effects of the friction charge induced by the DI rinsing. The key parameters of this experiment were revolution per minute (rpm) and time. An incubation time of above 10 sec was observed for the formation of Si pits and the rinsing time was more effective than rpm on the formation of the Si pits. The formation mechanism of the Si pits and optimized rinsing process parameters were investigated by measuring the charging level using a plasma density monitor. The DI rinse could affect the oxide substrate by a friction charging phenomenon on the photolithography process. Si pits were found to be formed on the micro structural defective site on the Si substrate under acceleration by developed and accumulated charges during DI rinsing. The optimum process conditions of DI rinse time and rpm could be established through a systematic study of various rinsing conditions.