Introduction The use of cut-outs in electron applicators make changes on output, isodose, and percentage depth dose (PDD) curves. These changes and electron beam dose distribution in the form of three-dimensional (3D) can be measured by gel dosimeters. Materials and Methods Dosimetry was performed with and without a square shield (6×6 cm2 field). The energies were 4, 9, and 16 MeV and phantom was filled with MAGIC gel polymer. For each section, transverse relaxation rate (R2) maps were obtained from MRI images and percentage depth doses and isodose curves were plotted. Results Average energy was 3.029 MeV for the energy of 4 MeV and 8.155 MeV for the energy of 9 MeV. Surface dose was higher in shielded field compared with the open one (due to electron scattering between the phantom and lead) which increased with increasing of energy. In the open field, for energies equal to 4, 9, and 16 MeV, the surface dose was 6.40, 6.48, and 7.20 Gy and for the shielded mode, they were 6.63, 7.04, and 7.31 Gy, respectively. Also error values showed less errors and higher accuracy on curves by increasing of energy. Conclusion Investigation of an isodose pattern in the shielded mode showed scattering due to the lead, which is on the applicator. Overall, the results of this study demonstrated the value and potential of this dosimetric method with respect to characteristics such as stability, responsiveness and specially ability to show three-dimensional electron beam dose distribution.