The electrowetting process is commonly used to handle very small amounts of liquid on a solid surface. This process can be modelled mathematically with the help of the shape optimization theory. However, solving numerically the resulting shape optimization problem is a very complex issue, even for reduced models that occur in simplified geometries. Recently, the second author obtained convincing results in the 2D axisymmetric case. In this paper, we propose and analyze a method that is suitable for the full 3D case.