Precisely characterizing epoxy/thermoplastic interfaces on the nanometer scale using scanning electron microscopy energydispersive X-ray (EDX) represents a current challenge due to the large X-rays generation volume, specimen decomposition, and related phenomena occurring with polymer samples. Interface characterization is, however, of high interest because the adhesion strength and overall performance of composites depend on the interface region. This work investigates the interface between an aerospace-grade epoxy based on a tetraglycidyl diaminodiphenyl methane/diaminodiphenyl sulphone (TGDDM/DDS) formulation and a semicrystalline fluoropolymer. Monte Carlo simulation is used in combination with EDX spot analysis to evaluate the effect of X-ray generation volume, charging, and phenomena arising from specimen decomposition. The results indicate that fluorine mobility due to specimen damage by electron beam irradiation is the principal factor affecting interface width measurements. An effective solution achieved by optimizing acquisition parameters and using an electron thin specimen allows accurate interface width measurement with a resolution of <300 nm.