Here's an example:
% create a figure with a couple of plots and save it to a .fig file:
f = figure();
subplot(2,1,1)
plot(1:10,1:10)
subplot(2,1,2)
plot(1:10,2:2:20)
saveas(f,'my_plots.fig')
% openfig() the .fig file and modify one of the axes YLim (note that
% ax(1) is the bottom axes and ax(2) is the top axes):
fig = openfig('my_plots.fig');
ax = findobj(fig,'Type','axes');
ax(2).YLim = ax(1).YLim;
