Ultrashort laser-induced modification of silicon is a process of great interest for future three-dimensional microelectronics, photodetectors and photovoltaics. Within the study of laser-induced nanostructures, sub-surface modifications of silicon have been observed by several authors. It has been proposed that the crystalline silicon is transformed into metastable polymorphic phases that could be attributed to stresses or high pressure waves [1]. Recently, it has been demonstrated that the surface morphology along with the femtosecond laser excitation of charge carriers plays an important role in the spatial modulation of the laser deposited energy [2]. In this work, we present a new possible explanation for this sub-surface modification based on an inhomogeneous absorption energy profile described by Mie scattering theory along with the free-carrier excitation. Finite Difference Time Domain (FDTD) simulations and Transmission Electron Microscopy (TEM) analysis suggest that the fs-laser-irradiated pre-structured surface acts as an assembly of microlenses which enhances the laser energy density at a micrometric range below the surface level and thus induce the local change of phase. The possibility of sub-surface modifications along with the transient change of the optical properties is thus demonstrated below the surface of nanostructured silicon. [1] M.J. Smith, E. Mazur et al, J. Appl. Phys. 110, 053524 (2011) [2] T. J.-Y. Derrien. Ph.D. thesis, Aix Marseille Université (Feb. 2012)