Ultrasonic standing waves with specific wavelengths generated in the multi-layered micro-resonators were numerically and experimentally analyzed. Using a three-dimensional scanning fluorescence microscope, the acoustophoretic motion of fluorescent microparticles within the micro-resonators was carefully and accurately measured. The manufactured micro-resonators were validated by comparing the location of the acoustic pressure nodal plane and the average energy density curves derived from numerical and experimental results. Results confirmed that the acoustic radiation force of the induced ultrasonic standing waves drives the microparticles vertically within the micro-resonators and their average energy density increases as the sinusoidal voltage applied to the piezoelectric transducer increases. Semi-empirical correlations were developed for the average energy density, based on experimental results for a wide range of the applied voltage amplitudes. The correlations were in good agreement, within less than 20 % of the experimental values measured for both the half-wavelength and quarter-wavelength micro-resonators.