I am not sure if I got exactly what you wanted but here goes a possible solution to your problem.
If you plotted using the hold on function I would therefore assume you have each contour in a different variable. If so you can use logic to check whether a contour is higher or lower relatively to another. If your problem is that you do not have the same x axis for each so that you can use logic just interpolate for each contour (for example between -0.8 and 0.8)
I will give an example of what I am saying. See if this helps.
%simulated contours
x=linspace(0,pi,100);
y = sin(x);
y2 = sin(x)*2;
y3 = sin(x)*3;
figure, hold on,
plot(x,y),
plot(x,y2),
plot(x,y3),
%fill contours
[X,Y]=meshgrid(x,0:3/100:3);
zzz=(Y<repmat(y,size(Y,1),1))+(Y<repmat(y2,size(Y,1),1))+(Y<repmat(y3,size(Y,1),1));
figure,imagesc(zzz)
set(gca,'YDir','normal')