Here's a little example of how you might do this with axes
to create an axis with a colored background and uistack
to move it to the back:
figure
h1 = subplot(2,2,1);
h2 = subplot(2,2,2);
h3 = subplot(2,2,3);
h4 = subplot(2,2,4);
p1 = get(h1,'Position');
p2 = get(h2,'Position');
border = 0.3*p1(1);
x1 = p1(1)-border;
y1 = p1(2)-border;
width1 = p2(3)+p2(1)-p1(1)+2*border;
height1 = max(p1(4),p2(4))+2*border;
ax1 = axes('Position', [x y width1 height1],...
'Color','r','XTick',[],'XColor','r','YTick',[],'YColor','r');
uistack(ax1,'bottom')
p3 = get(h3,'Position');
p4 = get(h4,'Position');
border = 0.3*p3(1);
x2 = p3(1)-border;
y2 = p3(2)-border;
width2 = p4(3)+p4(1)-p3(1)+2*border;
height2 = max(p3(4),p4(4))+2*border;
ax2 = axes('Position', [x2 y2 width2 height2],...
'Color','b','XTick',[],'XColor','b','YTick',[],'YColor','b');
uistack(ax2,'bottom')
This produces a figure that looks like this one :