Bulk acousti waves propagate in the bulk, as you mention nanoparticles positioning, surface acoustic waves may be more suitable to your application as they move the surface. Such surface acoustic waves are commonly produces by the use of IDT's (Inter-digited transducers).
However, aerial of fluidic acoustic waves can also help aligning nanoparticles. The medium (solid, liquid or gas) will matter in terms of frequency/wavelength due to the speed of sound related to it.