Try this:
% The inner box I want to fill with yellow color
% and outer box fill with blue color, but the axes should not be there.
x1=0;
x2=1;
y1=0;
y2=1;
x = [x1, x2, x2, x1, x1];
y = [y1, y1, y2, y2, y1];
r1 = [x1, y1, x2-x1, y2-y1]
x1=0.25;
x2=.75;
y1=0.25;
y2=.75;
x = [x1, x2, x2, x1, x1];
y = [y1, y1, y2, y2, y1];
r2 = [x1, y1, x2-x1, y2-y1]
% Plot them
rectangle('Position', r1, 'FaceColor', 'b')
hold on;
rectangle('Position', r2, 'FaceColor', 'y')
hold on
xlim([-1, 2]);
ylim([-1, 2]);
% Turn off the axes and tick marks
axis off;
