Electron beam irradiation of amorphous GeSe4 thin films reveals formation of reliefs and trenches as a function of electron beam dose. Mounds as high as 115 nm are observed at low electron beam dose and trenches as deep as 180 nm at high dose. The geometry of trench and mound formation is examined as a function of electron beam dose, film thickness, conductive overlayer thickness, exposure count, and beam step size. Thicker films are found to more likely form trenches than thinner ones. Physical mechanisms for trench and mound formation are proposed. Both types of deformations provide a route toward the direct write of optical waveguides, gratings, and waveguide-cavity coupled structures onto thin films of chalcogenide glass.