We report self-assembly of highly aligned GeTe nanowires epitaxially grown on octahedral GeTe microcrystals in two well-defined directions by using one-step vapor transport process. The epitaxial relationship of nanowires with underlying microcrystals along with the growth orientations of nanowires were investigated in detail by electron microscopy combined with atomic unit cell models. We demonstrate that maximizing atomic planar density to minimize energy of the exposed surfaces is the determining factor that governs the unique growth characteristics of micro/nanostructures that evolve from three-dimensional octahedral microcrystals to tetrahedral bases to finally one-dimensional nanowires. The crystallographic understanding of structuring of crystalline nanomaterials obtained from this study will be critical to understand, predict, and control the growth orientation of nanostructures in three-dimensions.