radiation (THz radiation) emission. [12][13][14] Partially amorphized Ge quantum dots encapsulated in the silicon matrix are proven to show an improved lasing action making them potentially useful for application in silicon integrated technology. [1,2] Enhanced molecular sensing capabilities have been demonstrated by plasmonenhanced infrared absorption due to an array of germanium nanostructures. [3,4] Arrays of GeSi nanostructures on silicon substrate showed an enhancement in the photo-voltage, showing promise for solar cell applications. [10] Surprisingly, germanium being an indirect bandgap semiconductor, periodic arrays of germanium nanostructures gave rise to THz radiation emission with comparable amplitude to the direct bandgap semiconductor n-GaAs (n-type GaAs). [13] Germanium nanostructures show threefold to fivefold increased amplitude of THz radiation emission as compared to the baregermanium surface. Local surface charge collection due to the high surface area is attributed to the enhanced THz emission from the Ge nanostructures. [12] These reports suggest that the periodic arrays of nanostructures play an essential role for improved light-matter interactions such as enhanced surface plasmon based sensing and improved terahertz emission. [3,4,13] The evolution of polygonal-shaped nanoholes on the (100) surface of germanium, aided by focused ion beam induced self-organization, is presented. The energetic beam of ions creates a viscous phase which, at a thermodynamical minimum, leads to surface self-organization. A directed viscous-flow along the predefined nanoholes provides well-ordered polygonal nanostructures, ranging from triangles to hexagons and octagons, as desired. The amorphization exhibiting a confined viscous-flow at the walls of nanoholes is attributed to the localized melting zones induced by sitespecific thermal spikes during ion irradiation, as revealed by microscopy and molecular dynamics studies. This leads to a local self-organization in the vicinity of each circular nanohole via a viscous-fingering process at the nanoscale. Such controlled self-organization, with the help of a predefined scanning grid, transforms the circular holes into the desired polygonal shape. The present morphology manipulation promises to surmount the barriers concerning the size reduction efforts in the field of nanofabrication.