This paper presents a detailed physical model for a novel method of two- and three-dimensional microstructure formation: dry electron beam etching of the resist (DEBER). This method is based on the electron-beam induced thermal depolymerization of positive resist, and its advantages include high throughput and relative simplicity compared to other microstructuring techniques. However, the exact mechanism of profile formation in DEBER has been unclear until now, hindering the optimization of this technique for certain applications. The developed model takes into account the major DEBER phenomena: e-beam scattering in resist and substrate, e-beam induced main-chain scissions of resist molecules, thermal depolymerization of resist, monomer diffusion, and resist reflow. Based on the developed model, a simulation algorithm was implemented, which allowed simulation of the profile obtained in resist by DEBER. Experimental verification of the DEBER model was carried out, which demonstrated the reliability of the model and its applicability for theoretical study of this method. The ultimate DEBER characteristics were estimated by simulation. The minimum line width and the maximum profile slope that could be obtained by DEBER were approximately 300 nm and 70°, respectively.