Two different orientations of an enzymatic biofuel cell (EBFC) chip, involving highly dense and three-dimensional cylindrical micro-electrodes arrays, have been studied with the finite element method. Mass transport phenomenon around the micro-electrodes of an EBFC chip inside a blood artery has been simulated. The stability of the chip to its position and blood flow pattern surrounding it are also investigated. The comparison between horizontal position (HP) and vertical position (VP) reveals that the chip can be more stable in VP rather than in HP. In VP, the diffusive flux and convective flux values are bigger compared to HP, but both these fluxes are non-uniform around all electrodes in both the positions. In addition to that in case of HP, the electrodes located at different positions on a chip receive different amount of glucose. A novel designed chip with holes through the substrate has enhanced the diffusive and convective flux in the HP of a chip and also all micro-electrodes on a chip receives similar amount of glucose uniformly throughout from the top to the bottom.