A method of purifying a sample in a two-phase system, comprising: providing a first liquid and a second liquid, the first liquid comprising a first fluid phase and an amount of a first molecule disposed in the first phase, the first phase having a first density, the second liquid comprising a second fluid phase, the second phase having a second density, the second density being different than the first density, the first phase and the second phase being immiscible; mixing the first liquid with the second liquid to form a mixture, the mixture comprising the first phase, the second phase, and the amount of the first molecule, at least some of the amount of the first molecule being disposed in the second phase of the mixture; allowing a first portion of the mixture to settle in a settling zone of a sample purification compartment to form a partially purified first phase sample portion and a partially purified second phase sample portion, characterized by: removing a portion of the partially purified second phase sample portion from the settling zone into a first acoustic settling loop (96, 97) that has opposing ends in fluid communication with the sample purification compartment, the removed portion of the partially purified second phase sample portion comprising a portion of the second phase, a portion of the amount of the first molecule, and a first number of first phase droplets, the first number of first phase droplets having a first average diameter; applying an acoustic wave to the removed portion of the partially purified second phase sample portion present inside the first acoustic settling loop (96, 97) to form a first acoustically treated sample portion, the first acoustically treated sample portion comprising a portion of the second phase, the portion of the amount of the first molecule, and a second number of first phase droplets, the second number of first phase droplets having a second average diameter, the second number being less than the first number, the second average diameter being larger than the first average diameter, the acoustic wave enhancing co-localization of at least a portion of the first number of first phase droplets, thereby enhancing coalescence of the at least a portion of the first number of first phase droplets; and re-introducing the first acoustically treated sample portion into the sample purification compartment. providing a first liquid and a second liquid, the first liquid comprising a first fluid phase and an amount of a first molecule disposed in the first phase, the first phase having a first density, the second liquid comprising a second fluid phase, the second phase having a second density, the second density being different than the first density, the first phase and the second phase being immiscible; mixing the first liquid with the second liquid to form a mixture, the mixture comprising the first phase, the second phase, and the amount of the first molecule, at least some of the amount of the first molecule being disposed in the second phase of the mixture; allowing a first portion of the mixture to settle in a settling zone of a sample purification compartment to form a partially purified first phase sample portion and a partially purified second phase sample portion, removing a portion of the partially purified second phase sample portion from the settling zone into a first acoustic settling loop (96, 97) that has opposing ends in fluid communication with the sample purification compartment, the removed portion of the partially purified second phase sample portion comprising a portion of the second phase, a portion of the amount of the first molecule, and a first number of first phase droplets, the first number of first phase droplets having a first average diameter; applying an acoustic wave to the removed portion of the partially purified second phase sample portion present inside the first acoustic settling loop (96, 97) to form a first acoustically treated sample portion, the first acoustically treated sample portion comprising a portion of the second phase, the portion of the amount of the first molecule, and a second number of first phase droplets, the second number of first phase droplets having a second average diameter, the second number being less than the first number, the second average diameter being larger than the first average diameter, the acoustic wave enhancing co-localization of at least a portion of the first number of first phase droplets, thereby enhancing coalescence of the at least a portion of the first number of first phase droplets; and re-introducing the first acoustically treated sample portion into the sample purification compartment.