You can either use the "rectangular", or export the data, use whatever the window function you want and do the integration. you can use script:
E1=getresult("mode1","E");
Ex=E1.Ex;
Ey=E1.Ey;
H1 = getresult( "mode1", "H" );
Hx=H1.Hx;
Hy=H1.Hy;
EH=pinch(Ex*conj(Hy)-Ey*conj(Hx));
x=E1.x;
y=E1.y;
then you can use a window function to further process the data.