In your script, as soon as you create the figure, set its visibility to off.
For example:
figure(28732);
set(28732,'visible','off'); %Now the figure is not shown
You can now work with the figure, plot, save etc, without the visual clutter or system overhead of displaying it.
If you want ALL of your figures to start without visibility, you can set the default property, as follows:
set(0,'DefaultFigureVisible','off').
This will cause all generated figures to be generated without visibility. (Note, this will be very confusing is you forget that this property is set.)
You should still close the figure as soon as possible in the script, as a part of good memory management.