We present evidence that the penetration of electrons in solids, typically a few micrometers at the usual acceleration voltages used in electron microscopes, influences the shape of sub-microstructures created by focused electron beam induced deposition. We demonstrate how monitoring the sample current during deposition gives information on the electron scattering. A physical model is proposed and checked on a series of structures ranging from films to tips and complex 3D shapes. This method provides an efficient quality control tool for the process, witnesses the deposition sequence, and offers a signature of the electron scattering in microstructures.