Biological structures are progressively serving as inspiration for new and improved materials and technologies. The microstructures of many biomineralized tissues, such as bone, exoskeleton, and nacre, are highly ordered and contain at least one stiff phase and one soft phase. This results in strong and tough materials, which can be synthetically replicated and used to improve coatings, armor, and other technologies. In this study, we emulate the brick-and-mortar structure of nacre by ordering anisotropic microparticles in a microfluidic channel. Ordering and filtering are performed via acoustophoresis, in which particles in the microfluidic channel migrate in response to a standing pressure wave. Filtering efficiency is described as a function of flow rate, piezoelectric power, particle shape/size, and initial volume fraction. In general, low flow rate and high piezoelectric power resulted in the highest filtering efficiency.  Additionally, we explored patterning and self-assembly of microrods into columns under piezoelectric excitation, and found the columnar spacing to be a function of the number of columns, but independent of piezoelectric power. This project has applications in additive manufacturing technologies for the production of highly ordered, high volume fraction, anisotropic two-phase structures.