Hmm, maybe 'findobj' could work. I tried some code that seemed to work:
% Find all figures
list_of_figs = findobj('type','figure');
% The latest opened figure, should be in the end of the list.
sub_fig = list_of_figs(end);
% Close the figure
close(sub_fig);
Or you could open you sub GUI's using the same name for all of them (since you won't have more than one open at a time anyway), and then just use close(sub_fig_name).
