Polymer nanocomposites containing nanoscale fillers are an important class of materials due to their ability to access a wide variety of properties as a function of their composition. In order to take full advantage of these properties, it is critical to control the distribution of nanofillers within the parent polymer matrix, as this structural organization affects how the two constituent components interact with one another. In particular, new methods for generating ordered arrays of nanofillers represent a key underexplored research area, as emergent properties arising from nanoscale ordering can be used to introduce novel functionality currently inaccessible in random composites. The knowledge gained from developing such methods will provide important insight into the thermodynamics and kinetics associated with nanomaterial and polymer assembly. These insights will not only benefit researchers working on new composite materials, but will also deepen our understanding of soft matter systems in general. In this review, we summarize contemporary research efforts in manipulating nanofiller organization in polymer nanocomposites and highlight future challenges and opportunities for constructing ordered nanocomposite materials.