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High aspect ratio submicron trench cleaning is of seriously concern in semiconductor manufacturing. Megasonic cleaning is known as one of the most effective techniques in blanket wafer cleaning. The authors have studied megasonic rinsing and cleaning processes for blanket wafers and provided both experimental and modeling results. Although megasonic cleaning is currently used in patterned wafer cleaning, the mechanism of the process is not well understood. In our previous research , simulation of pulsating flow passing a series of rectangular cavities was verified and showed excellent agreement with the numerical and experimental results of Perkins. Pulsating flow rinse shows a significant advantage in patterned wafer cleaning because the vortex oscillating mechanism enhances the mixing. In this paper, the removal of contaminants from high aspect-ratio submicron trenches using high frequency pulsating flow (megasonic rinse) is studied using physical modeling.