To understand the NF3/NH3 dry cleaning mechanism, we have investigated the dry cleaning process with different Si-based materials, Si, SiO2, and Si3N4 using atomic force microscopy (AFM), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and x-ray photoelectron spectroscopy (XPS) in terms of surface modification. In this paper, we report that the NF3/NH3 dry cleaning process using down-flow plasma technique can cause significant surface modification on SiO2 depending on the NF3:NH3 ratio and plasma power of the plasma reaction before (NH4)2SiF6 by-product sublimation step. These results might provide empirical evidence that there are competing reaction pathways producing different intermediate species on SiO2 surface to form (NH4)2SiF6 by-product depending on the process conditions. A possible mechanism is presented.