In the conventional wet cleaning process of contact holes landing on the Si substrate and WSi metal gate, the ILD BPTEOS bowing and CD enlargement were often found by using dilute HF solution. With the device design rule decreasing, the CD size control and cleaning efficiency enhancement are highly demanded. In this work, the high aspect-ratio contact (AR~10) cleaning in single wafer (SW) tool was demonstrated in 58nm flash device. With the facilitation of nano-spray function to enhance particle removal efficiency (PRE), AM1 cleaning in SW tool can achieve the low contact resistance and tighten Rc distribution with less ILD film damage and lower CD enlargement. The parameter dependency of SW tool, including chemical injection method, nozzle swinging effect and nano-spray function, on contact resistance was also investigated. Compared to AM1 cleaning in bench tool, AM1 process in SW tool performs the larger process window for less ILD film damage at higher temperature and concentration.