Doping of silicon with chalcogens (S, Se, Te) by femtosecond laser irradiation to concentrations well above the solubility limit leads to near-unity optical absorptance in the visible and infrared (IR) range and is a promising route toward silicon-based IR optoelectronics. However, open questions remain about the nature of the IR absorptance and in particular about the impact of the dopant distribution and possible role of dopant diffusion. Here we use electron tomography using a high-angle annular dark-field (HAADF) detector in a scanning transmission electron microscope (STEM) to extract information about the three-dimensional distribution of selenium dopants in silicon and correlate these findings with the optical properties of selenium-doped silicon. We quantify the tomography results to extract information about the size distribution and density of selenium precipitates. Our results show correlation between nanoscale distribution of dopants and the observed sub-band gap optical absorptance and demonstrate the feasibility of HAADF-STEM tomography for the investigation of dopant distribution in highly-doped semiconductors.