In this study, a cleaning method for pregate cleaning which can suppress the generation of the microroughness of silicon-wafer surfaces as well as remove various contaminations such as metallic impurities, organic materials, and particles has been investigated. Functional waters such as ozonized ultrapure water (O-3-UPW), H-2-added UPW (H-2-UPW), and low-concentration HF and hydrogen peroxide (H2O2) solution have been used in this cleaning method at room temperature. The cleaning-process flow is as follows: (i) O-3-UPW cleaning, (ii) diluted HF and H2O2 mixture including surfactant molecules (FPMS) cleaning with megasonic, and (iii) 30%-isopropyl alcohol/UPW rinsing, i.e., realization of three-step cleaning. After the pregate cleaning, silicon substrates are set into the radical-reaction gate-insulator film-formation process using microwave-excited, high-density plasma equipment, where Kr+ or Xe+ ion bombardment onto the substrate surface has been introduced to eliminate absorbed surfactant molecules as well as hydrogen termination, before starting oxygen radical oxidation (Kr/O-2) or NH* radical nitridation (Xe/NH3). This advanced, three-step room-temperature cleaning is promising for future semiconductor manufacturing in conjunction with the newly developed radical-reaction-based semiconductor manufacturing.