One of the major challenges in nuclear fusion, nanolithography, and various industries is the effect of low energy ion irradiation on the surface morphology of materials. For example, the effect of low energy irradiation on plasma-facing materials' lifetime in fusion reactors, the effect on the optical systems in nanolithography laser produced plasma devices, and the effect on mass production of effective and flexible anti-reflecting coatings in photovoltaic (PV) industry. Silicon and carbides in particular, showed interest in nuclear fusion as potential wall materials, as in mirror designs for nanolithography devices, and as coatings in PV system components. Recently innovative novel Si nanostructures such as nanocones (NCs) demonstrated great feasibility in several areas including the next generation PV cells, batteries, supercapacitors, nano-optoelectronics, photonics, and energy storage devices. Their unique electronic properties and significantly higher absorption over a wide broadband range, offer paramount potential in various fields including microelectronics, optoelectronics, photonics, photovoltaics, biology, sensors, templet for selective growth (on nanostructured substrates), fast electronic devices, and even in high- density data storage. We tailor Si NCs using simultaneous low energy helium (He) ion irradiation on planar Si (111) and (100) and Ta metal masks. In a series of successive experiments, three key parameters, temperature, flux, and presence of Ta metal impurity, were tuned to study the progression of nanostructure development, as well as the effect of these nanostructures on key material properties. Before performing He ion sputtering experiments, 100 eV Ar+ ion irradiations, for 10 min duration, were also performed in-situ in each case for removing any preexisting SiO2 form planer Si substrates. Clear and distinctive progressions of NC development were found during the tuning of each parameter. During the temperature dependent studies, we clearly observed a sequential progression from thicker and less dense cones (773 K) to finer and more densely packed NCs (1073 K). On the other hand, during the case of flux dependent studies, it was found that increasing flux increases the size of the NCs, with low flux resulting in sparsely placed nanodots, and high fluxes resulting in large conglomerates. Finally, the effect of Ta impurity shows an increased propensity for NCs development. In addition, using optical-reflectivity studies we clearly observed a significant reduction (from ∼65 to almost zero) in optical reflectivity.