To avoid showing figures in MATLAB you can start MATLAB using the noFigureWindows option. This option is not available on UNIX.
matlab -noFigureWindows
As an alternative you can change the default figure properties of the MATLAB root object:
set(0,'DefaultFigureVisible','off')
If you want to temporarily suppress new figures that should be accesable later in the same session you can save the figure handle:
set(0,'DefaultFigureVisible','off');
%create invisible figure 1
h(1)=figure;
%create invisible figure 2
h(2)=figure;
set(0,'DefaultFigureVisible','on');
%show figure 1
figure(1)
