Integrated electronics, photonics and optoelectronics need full control of lattice reconstruction processes in silicon nanostructures at the nanoscale level. However, conventional thermal treatments do not meet the challenging requirements necessary for developing next-generation devices. Light can be a powerful tool to trigger and control opto-thermal effects in resonant nanostructures. Here we propose a new computational approach to light-matter interactions in silicon nanopillars, which simulates heat generation and propagation dynamics occurring in continuous wave laser processing over a wide temporal range (from 1 fs to about 25 hours). We demonstrate that a rational design of the nanostructure aspect ratio, type of substrate, laser irradiation time and wavelength enables amorphous-to-crystalline transformations to take place with a precise, sub-wavelength spatial localization. In particular, we show that visible light can be exploited to selectively crystallize the internal region of the pillars, which is not possible by conventional treatments. A detailed study on lattice crystallization and reconstruction dynamics reveals that local heating drives the formation of secondary antennas embedded into the pillars, highlighting the importance of taking into account the spatial and temporal evolution of the optical properties of the material under irradiation. This approach can be easily extended to many types of nanostructured materials and interfaces, offering a unique computational tool for many applications involving opto-thermal processes (fabrication, data storage, sensing, catalysis, resonant laser printing, opto-thermal therapy, etc.…).