It is known that polymers mostly shrink during observation by scanning electron microscope. However, resist surface deformation during electron beam irradiation has not been discussed in electron beam lithography. In the present study, poly(methyl methacrylate) (PMMA) film is taken as an example of polymers, and the surface deformation by electron beam irradiation is measured by atomic force microscope. Exposure dose varies in a range to obtain the exposure intensity distribution (EID) curve for point exposure, that is from 10-11 to 10-6 C at an acceleration voltage of 20 kV. Even at a dose of 5×10-10 C, where a contribution of backscattered electrons from the Si substrate becomes significant in the distribution, a dimple of around 1 µm radius and around 30 nm depth is produced. The EID curve derived from the experiment might be influenced by the deformation. Assuming that the development process starts from this deformed surface, it should be a serious problem in lithography, especially for low-sensitivity resists. The deformation is not only shrinkage, but also deposition along the beam axis for the resists. In the present study, the surface deformation is analyzed in terms of the electron-beam-induced shrinkage and deposition. A simulation model is presented to quantify the mechanism, and the range of its validity is discussed.