Exposing cells to ultrashort electric field pulses can lead to the permeabilization of the membranes of the internal cell organelles, such as the nucleus, which is termed as supra-electroporation. In this paper, we study the supra-electroporation of stem cells with realistic morphologies under nanosecond electrical pulse stimulation. For such short pulses, the cell and the nucleus membranes exhibit non-linearity in their conductance. Therefore, we used a non-linear model for the cells' membranes, coupled with a quasi-static electromagnetic solver, and obtained the solution using a commercial Finite Element Method (FEM) solver. The results show that the outer shape of the cell has a strong effect on the magnitude and the spatiotemporal patterns of the electric field inside the cell, which affects the rate of the supra-electroporation of the nucleus. These variations in the rate of the supra-electroporation of the nucleus can guide the selective targeting of desired cells with specific shapes.