In the present study, a 3D device-level numerical model is implemented via finite element method to assess the effects of design and operating parameters on the separation performance of a microscale acoustofluidic device. Elastodynamic equations together with electromechanical coupling at the piezoelectric actuators for the stress field within the solid parts, Helmholtz equation for the acoustic field within fluid, and Navier-Stokes equations for the fluid flow are coupled for the simulations. Once the zero-acoustic and flow fields are obtained, the trajectories of the particles are obtained by employing point-particle approach. The particle trajectories are simulated for many particles with different sizes released from random initial locations. Separation performances of the different cases are evaluated based on described metrics such as purity, yield, percentage of particle stuck in the channel, the force acting on the particles, residence time and separation parameter.