The characteristics of an electrode are defined by the characteristics of the material used to develop it. In this paper, we focus on the fabrication of cylindrical 3-dimensional Glassy Carbon microelectrode arrays (MEAs) for analyzing cell preparations from cardiac tissues. In order to improve the electrical properties of the commercially available electrodes, we have used a highly conductive material for fabrication. Glassy Carbon microelectrodes were fabricated by the pyrolysis of SU-8 microelectrodes which were developed by a standard lithographic process on Silicon wafer. The ohmic nature and high conductivity of Glassy Carbon makes it a suitable material to be implemented in electrophysiological studies. Further in our work, we have performed the theoretical and structural analysis using Comsol Multiphysics 5.2 considering different geometries of microelectrodes. The skin insertion force is calculated to be 0.012N, which is much lesser than the comprehensive force (15.38N), the maximum bending force (0.885N) and the maximum buckling force (3.28N) per cylindrical microelectrode. The maximum Von Mises stress (as shown in the figure) acting at the base where it is attached to the substrate is found out to be 6.56x106 N/m2 for each cylindrical microneedle. Among all the considered geometries, it can be concluded that the fabricated cylindrical microelectrodes penetrate successfully without breaking or bending and causing minimal damage to the cardiac tissues. The slanted tip microelectrode was also favored as it’s design makes it able to easily pierce the cardiac cell layers. However, the Maximum Von Mises stress distribution showed that the stress at the tip was much higher than the Yield strength of Glassy Carbon (4Gpa) making it evident that the tip might break while penetrating. With the theoretical and simulation analysis performed we were thus able to optimize the geometry and establish that Glassy Carbon proves to be a good material for fabrication of 3D microelectrode arrays.