We apply second order finite difference to calculate the lowest eigenvalues of the Helmholtz equation, for complicated non-tensor domains in the plane, using different grids which sample exactly the border of the domain. We show that the results obtained applying Richardson and Pad\'e-Richardson extrapolation to a set of finite difference eigenvalues corresponding to different grids allows to obtain extremely precise values. When possible we have assessed the precision of our extrapolations comparing them with the highly precise results obtained using the method of particular solutions. Our empirical findings suggest an asymptotic nature of the FD series. In all the cases studied, we are able to report numerical results which are more precise than those available in the literature.