From 2D created in PDE Tool box to 3D

HelLo, I have been working with the PDE Tool box. I am trying to calculate capacitance by solving Poissons Equation, using the PDE tool box. I have been successful in calculating it by exporting the values from the tool box to the workspace window,and then using :

function energy = calcEnergy(p,t,permittivity,u)
[dudx,dudy] = pdegrad(p,t,u);
[area] = pdetrg(p,t);
energy = permittivity*sum(area.*(dudx.*dudx + dudy.*dudy))/2;
end

This gives me the energy, and I can just multiply by 2, and divide by the Voltage^2. But now I need to represent that in 3D. I don't know if what I get from the PDE tool box is helpful at all, seeing how its 2D, would I need to start from scratch using script? Also, I get the right values imagining that I have an ideal capacitor, but my project involves a non-ideal capacitor. Any one has any idea of how to represent this? my matlab knowledge is very limited, so please be very specific with the answers.

Thanks Alejandra