The difference between ultrasonic cleaning and megasonics cleaning lies in the frequency that is used to generate the acoustic waves. Ultrasonic cleaning uses lower frequencies; it produces random cavitation. Megasonics cleaning uses higher frequencies at 1000 kHz; it produces controlled cavitation.

An important distinction between the two methods is that the cavitation effects in a megasonic bath are much less damaging than those found with ultrasonic frequencies. This significantly reduces or eliminates cavitation erosion and the likelihood of surface damage to the product being cleaned. Parts that would be damaged by ultrasonic frequencies or cavitation effects can often be cleaned without damage in a megasonic bath using the same solution.

With ultrasonics, cavitation occurs throughout the tank, and all sides of submerged parts are cleaned. With megasonics, the acoustic wave is found only in a line of sight from the transducer surface. For this reason megasonic transducers are typically built using arrays of square or rectangular piezo devices bonded to a substrate and spaced as close together as possible. Semiconductor wafers are typically cleaned in carriers holding the substrates perpendicular to the transducer so that both front and back surfaces can be cleaned. Special carriers are sometimes used to reduce any obstructions that may prevent parts of the wafer surface from being cleaned.