Bismuth chalcogenides belong to the group of materials that can make future electronic devices far more powerful than today. However, nanostructurization of those materials is still a challenging process, as the quality of the structure surface will affect the material behavior. Our research is centered on defects induced in chalcogenides (Bi₂Se₃ and Bi₂Te₃) by the structurization process using Focused Ion Beams, by means of XAS, TEM and magnetoresistance studies. The fundamental goal of the study is to optimize the parameters of lithography processes (beam current, kinetic energy of ions, time of exposure, etc.) in order to keep the minimal desired size and shape of the nanostructures and preserve topological insulators properties by minimizing the damage in the surface states induced by the impinging ions.