A method for cleaning semiconductor substrate without damaging patterned structure on the substrate using ultra/mega sonic device comprising applying liquid into a space between a substrate and an ultra/mega sonic device; setting an ultra/mega sonic power supply at frequency f1 and power P1 to drive said ultra/mega sonic device; before bubble cavitation in said liquid damaging patterned structure on the substrate, setting said ultra/mega sonic power supply at frequency f2 and power P2 to drive said ultra/mega sonic device; after temperature inside bubble cooling down to a set temperature, setting said ultra/mega sonic power supply at frequency f1 and power P1 again; repeating above steps till the substrate being cleaned. Normally, if f1=f2, then P2 is equal to zero or much less than P1; if P1=P2, then f2 is higher than f1; if the f1