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Transcutaneous Electrical Stimulation (TES) has been used widely to recover motor functions in neurologically impaired individuals by artificially activating skeletal muscles using superficial electrodes. Some simulation studies have investigated the percentage of fibers activated in denervated skeletal muscles, the comfort and selectivity, and the influence of fat thickness in the case of obese people, to optimize the inter-electrode distance and electrode size. However, the effect of the inter-electrode distance, electrode shape and electrode size might be further analyzed using the selectivity, activation depth and activation volume. In this regard, we developed a 3D multi-layer (skin, fat, muscle, and nerve) thigh model coupled with a mammalian nerve model using a finite element method for optimization of TES therapy. Different evaluation indices (motor threshold, activation depth, selectivity and activation volume) were inspected to compare different TES parameters in terms of nerve activation. The simulation results agreed with experimental data and new insights were obtained: selectivity is better in small electrodes; nevertheless, in high current stimulation, small electrodes and large electrodes have similar selectivity.