Acoustophoresis is generation of force fields by using sound waves. In microfluidics, micro-scale fluid cavities are used to handle fluids and particle suspensions. The sub-millimeter wavelength of ultrasound waves is suitable for exciting resonant acoustic fields in microfluidic devices. Combining acoustophoresis with microfluidics has resulted in emergence of the rapidly growing field of acoustofluidics. Acoustophoretic particle manipulation is an active, contact and label free method for handling microparticles that is easily integrated into microfluidic systems. Due to gentle and robust manipulation and excellent cell viability, acoustofluidic devices are attractive tools for miniaturization in life science fields. These applications include cell handling, sorting, washing and patterning toward bio-3D-printing. In addition, acoustic particle manipulation has gained popularity for creating microstructures and particle assemblies. This is aimed towards improved additive manufacturing and 3D printing of functionalized composite materials.The underlying physics of acoustofluidics is not intuitively understood because of complex interplays between various solid, piezoelectric and fluid components. Theoretical framework gives a general understanding of fundamental acoustic principles limited to simple physics and geometries. It is extremely cumbersome to modify analytical methods to fit the engineering needs of modern acoustofluidics. Experimental research provides specific insight at a high cost while limited by characterization techniques. Numerical modeling is useful for gaining in-depth understanding of acoustophoresis. Finite Elements Method simulations are developed from first principles to solve governing equations of acoustofluidic systems. This provides a detailed understanding of acoustic effects beyond simple assumptions and geometries. In this thesis, numerical modeling and validating experimental methods are used to contribute to detailed understanding of acoustofluidics. Informed by this, engineering solutions are proposed to improve acoustofluidics where limitations constrain applications. Acoustofluidics rely on resonances to concentrate acoustic energy in the desired manipulation regions. Simulations show that geometrically asymmetric architecture increases the acoustic resonance amplitude by almost two orders of magnitude. This is achieved in Bulk Acoustic Wave devices using a half-wave standing pressure field. Experiments with silicon-glass devices show a significant improvement in acoustophoresis of 20-micron silica beads in water when asymmetric devices are used. The so-called acoustic radiation force is a result of scatter-incident acoustic interference. Finite Element Method is used to find resonant modes, damping factors and acoustic forces of an elastic sphere subject to a standing acoustic wave. Under fundamental spheroidal modes, the radiation force fluctuates significantly around analytical values due to constructive or destructive scatter-incident wave interference. This suggests that for certain materials, relevant to acoustofluidic applications, particle resonances are an important scattering mechanism and design parameter. These findings offer the potential to manipulate and separate microparticles based on their resonance frequency. Particle translation is a result of acoustic radiation force which is defied by the viscous drag on the particle surface. Additionally, non-spherical suspended objects experience acoustic radiation and viscous torques that induce rotation. Numerical simulations of acoustic radiation force and torque on these particles show that they rotate to reach a single preferred orientation. Controlling particle orientation adds a degree of freedom to acoustophoretic manipulation. This also informs assembly patterns of non-spherical microparticles.