A flow-through ultrasonic separator is a novel type of separation device concentrating and separating suspended micro-particles from within a liquid in a standing ultrasonic field. It can accomplish a fast, sharp, efficient and controllable separation of micro-particles in a liquid suspension. The thesis focuses on modelling the electro-acoustic characteristics of flow-through ultrasonic separators with a special emphasis on analysing and designing the MEMS micromachined ultrasonic filter in an EPSRC and DSTL funded project. Based on the model results, a micromachined ultrasonic filter is designed and built using micromachining processes. The verification of the model against the fabricated device is made. A comparison of the predicted impedance results and the experimental measured results indicates a good match. It shows that the model can give high confidence in predicting the electro-acoustic characteristics and the filtration performance. The thesis uses an equivalent-circuit transducer model, coupled with acoustic impedance transfer relationships to analyse the transducer and cavity resonance model, and to investigate such ultrasonic separators with regards to the electro-acoustic characteristics of the resonator under different conditions. In particular, the influence of matching layer thickness and reflector thickness on the stored energy-frequency product of the layered resonator are examined in the cases of cells with a variety of transducer and cell characteristics. The thesis infers the acoustic force transfer equations and the acoustic pressure and velocity equations in the multi-layered resonator both with a rigid reflector and with an arbitrary termination. The stored energy-frequency product and the acoustic pressure distribution in the fluid chamber of the ultrasonic filters are investigated in detail. The modelled results regarding the electro-acoustic characteristics and the filtration performance of the resonator system in the ultrasonic separators have been satisfactorily validated by experimental measurement results in different ultrasonic separators. Research results show that the model can be used to tune the performance of flow-through ultrasonic separators by optimising the design of such efficient transducer resonators. Therefore, it can be widely used to predict the resonant behaviour as a result of modifications to a variety of multi-layered resonators of the ultrasonic separators.