Acoustophoresis which means separation of particles and cells using acoustic waves is becoming an intensive research subject. The method is based on inducing an ultrasonic compression standing wave inside a microchannel. A finite element approach is used to model the acoustic and electro-mechanical behavior of the piezoelectric material, the micro-channel geometry as well as the fluid inside the channel. The choices of silicon and PDMS materials are investigated as the chip materials for the resonator. A separation channel geometry which is commonly used in the literature is implemented in this study and the fluid flow inside the microchannel geometry is simulated using computational fluid dynamics. The acoustic field inside the fluid channel is also be simulated using the finite element method. For the separation process to be successful micro-particles of different diameter groups should end up in different channels of the micro-separator. In order to simulate real life scenarios, each particle size group have a size distribution within themselves. For realistic simulation results the particles will be released into the micro separator from a different starting locations (starting location distribution). The results of this Monte-Carlo based finite element simulation approach will be compared with the reported experimental results.