A finite-element model is presented for numerical simulation in three dimensions of acoustophoresis of suspended microparticles in a microchannel embedded in a polymer chip and driven by an attached piezoelectric transducer at MHz frequencies. In accordance with the recently introduced principle of whole-system ultrasound resonances, an optimal resonance mode is identified that is related to an acoustic resonance of the combined transducer-chip-channel system and not to the conventional pressure half-wave resonance of the microchannel. The acoustophoretic action in the microchannel is of comparable quality and strength to conventional silicon-glass or pure glass devices. The numerical predictions are validated by acoustic focusing experiments on 5-μm-diameter polystyrene particles suspended inside a microchannel, which was milled into a polymethylmethacrylate chip. The system was driven anti-symmetrically by a piezoelectric transducer, driven by a 30-V peak-to-peak alternating voltage in the range from 0.5 to 2.5 MHz, leading to acoustic energy densities of 13 J/m3 and particle focusing times of 6.6 s.