Self-assembled nanofibers of peptide-amphiphile molecules have been of great interest because of their bioactivity both in vitro and in vivo. In this work, we demonstrate the simultaneous self-assembly, alignment, and patterning of these nanofibers over large areas by a novel technique termed sonication-assisted solution embossing. In this soft lithographic technique, the nanostructures self-assemble by solvent evaporation while under the influence of ultrasonic agitation and confinement within the topographical features of an elastomeric stamp. The nanofibers orient parallel to the channels as they assemble out of solution, yielding bundles of aligned nanofibers on the substrate after the stamp is removed. Alignment is likely a result of steric confinement and possibly a transition to a lyotropic liquid crystalline phase as solvent evaporates. This technique is not limited to uniaxial alignment and is shown to be able to guide nanofibers around turns. Alignment of nanostructures by this method introduces the possibility of controlling macroscale cellular behavior or material properties by tuning the directionality of interactions at the nanoscale.