So you want to be able to see a smaller polygon inside a bigger one?
Use the facealpha and edgealpha properties to make the larger patch object more translucent and the inside one less translucent.
%Rendering overlay example
I1 = false(100,100,100); %First image
I1(10:90,10:90,30:70) = true; %make rectangular part of I true
[xx yy zz] = meshgrid(1:100,1:100,1:100); %second image sphere with radius 10 centered at (50,50,50)
I2 = sqrt((xx-50).^2+(yy-50).^2+(zz-50).^2)<10;
fv1 = isosurface(I1,0); %Make the triangles
fv2 = isosurface(I2,0);
%Blue ball inside light green box
figure; hold on
patch(fv1,'facecolor',[0 1 0],'facealpha',0.3,'edgecolor','none');%[.5 .5 0],'edgealpha',0.3);
patch(fv2,'facecolor',[0 0 1],'facealpha',0.7,'edgecolor','none');
view(19,28)
