A system set up for use as a perfusion reactor comprising: A) a bioreactor including a reaction vessel having an internal volume, an agitator for circulating a fluid medium comprising desired product and cells within the internal volume, a feed inlet, and an outlet; and B) an acoustophoretic filtering device fluidly connected to and downstream of the bioreactor, the acoustophoretic filtering device comprising: 1) an inlet fluidly connected to the bioreactor outlet for continuously receiving fluid medium from the bioreactor; 2) a flow chamber through which the fluid medium can flow; and 3) a sleeve surrounding the flow chamber, the sleeve including an ultrasonic transducer and a reflector located opposite the ultrasonic transducer, the ultrasonic transducer being driven to produce a three-dimensional acoustic standing wave in the flow chamber that separates the desired product from the cells; and 4) a product outlet for removing a concentrated flow of the desired product; 5) a recycle outlet for sending the fluid medium back to the bioreactor, the recycle outlet located downstream of the flow chamber and connected to a recycle inlet of the reaction vessel wherein the acoustophoretic filtering device is configured so that the three-dimensional acoustic standing wave has an axial force component and a lateral force component which are of the same order of magnitude and results in an acoustic radiation force that is larger than the combined effects of fluid drag and buoyancy or gravity, and is therefore able to trap the cells to allow more time for the acoustic wave to increase particle concentration, agglomeration and/or coalescence. A) a bioreactor including a reaction vessel having an internal volume, an agitator for circulating a fluid medium comprising desired product and cells within the internal volume, a feed inlet, and an outlet; and B) an acoustophoretic filtering device fluidly connected to and downstream of the bioreactor, the acoustophoretic filtering device comprising: 1) an inlet fluidly connected to the bioreactor outlet for continuously receiving fluid medium from the bioreactor; 2) a flow chamber through which the fluid medium can flow; and 3) a sleeve surrounding the flow chamber, the sleeve including an ultrasonic transducer and a reflector located opposite the ultrasonic transducer, the ultrasonic transducer being driven to produce a three-dimensional acoustic standing wave in the flow chamber that separates the desired product from the cells; and 4) a product outlet for removing a concentrated flow of the desired product; 5) a recycle outlet for sending the fluid medium back to the bioreactor, the recycle outlet located downstream of the flow chamber and connected to a recycle inlet of the reaction vessel 1) an inlet fluidly connected to the bioreactor outlet for continuously receiving fluid medium from the bioreactor; 2) a flow chamber through which the fluid medium can flow; and 3) a sleeve surrounding the flow chamber, the sleeve including an ultrasonic transducer and a reflector located opposite the ultrasonic transducer, the ultrasonic transducer being driven to produce a three-dimensional acoustic standing wave in the flow chamber that separates the desired product from the cells; and 4) a product outlet for removing a concentrated flow of the desired product; 5) a recycle outlet for sending the fluid medium back to the bioreactor, the recycle outlet located downstream of the flow chamber and connected to a recycle inlet of the reaction vessel