This enhancement has been incorporated in Release 2011b (R2011b). For previous product releases, read below for any possible workarounds:
You can export your data to MATLAB and use the SIMPLOT command to plot your data from MATLAB. This will generate a MATLAB figure that will allow you to change the figure properties. For more information, type 'help simplot' at the MATLAB command window prompt.
If you need to manipulate the Scope window for simulation, you can use the following snippet of code:
shh = get(0,'ShowHiddenHandles');
NOTE: Simulink does not support manipulating graphics properties using the Scope or Signal Viewer handle. When manipulating any graphics properties, do not change or alter the structure of the scope. For example, you should not delete any of the graphical objects (text, axes, menus, etc) in the scope as this could lead to unstable behavior.