One embodiment of the present invention is a method for characterizing an electron beam treatment apparatus that includes: (a) e-beam treating one or more of a predetermined type of wafer or substrate utilizing one or more sets of electron beam treatment parameters; (b) making post-electron beam treatment measurements of intensity of a probe beam reflected from the surface of the one or more wafers in which thermal and/or plasma waves have been induced; and (c) developing data from the post-electron beam treatment measurements that provide insight into performance of the electron beam treatment apparatus.