If you can reproduce the figure, just save the coordinates in addition to plotting them,
plot(x,y,'o')
save('coordinates.mat','x','y')
If you only have the .fig file and need to extract the coordinates, open the file so it's the current figure,
fig = gcf();
ax = gca(fig);
chil = ax.Children;
x = get(chil,'XData');
y = get(chil,'YData');
z = get(chil,'ZData');
x,y,z, will be vectors if only 1 set of data are plotted on the axes. If more than 1 object is plotted, x,y,z will be a n*1 cell array for n objects.
