Focused ion beam coupled with scanning electron microscopy (FIB-SEM) is a popular technique for advanced electron microscopy with applications such as, high-precision site-specific lamella sample preparation for transmission electron microscopy (TEM) and slice-and-view FIB 3-dimensional tomography. Damage caused by the electron imaging component of FIB-SEM may be compounded with damage from the ions during the ion milling process. There are known strategies for mitigating damage from ions and electrons (cryo-SEM, dose-control, voltage control), but the electron damage on common embedding resins for EM has not been explored in detail beyond their resistance to shape-change. The relationship between beam parameters and damage mechanisms remains unclear. Since we are relying on the physical, chemical and thermal stability of embedded samples during ion-beam milling, it is important to distinguish electron beam damage from ion beam damage. Scanning transmission X-ray microscopy (STXM) has been used for analyzing the electron beam radiation damage on polymer films by characterizing the chemical bonding changes. In this paper, we focus on the effect of beam voltage and electron dose on electron beam damage to epoxy resin thin films. Irradiated areas on polymer thin films were characterized by near edge X-ray absorption fine structure (NEXAFS) in STXM. We found that, even when using low current and voltage, the electron beam can still cause noticeable chemical changes within the polymer film. The degree of electron beam damage depends not only on the beam energy, but also on the amount of inelastic scattering occurring within the material, as determined by the sample thickness.