Here is how to grab a handle to an open instance of STK, or how to create an instance of STK from MATLAB using the COM interface.
%if STK is not open..
%start it all off - create COM object
uiApplication = actxserver('STK11.application');
%if STK is open...
uiApplication = actxGetRunningServer('STK11.application');
%get the object model root
root = uiApplication.Personality2;
You can learn more using STK and MATLAB together in the STK Help at STK Help > Integrating with STK > MATLAB Interface
and in the Integrating STK and MATLAB FAQ