For high precision micromachining of micro- and nanostructures by focused ion beams, the precision of the material removal process is of great importance. In this article, the topological properties of the ion beam generated structures like slope angles of trenches, surface roughness, and induced defects are investigated. The influence of the beam current and scanning strategy on the topological properties will be discussed, In addition, transmission electron microscopy analysis of thin lamellas generated by focused ion beams will be shown.