I found the answer myself from matlab help. it can be set or reset using "set_param" command. an example is given below
open('MyModel.mdl');
set_param('MyModel/3-Phase Fault', 'FaultA', 'on');
here "3-Phase Fault" is the name i gave to the block in "MyModel.mdl". "FaultA" is the parameter name (Default). To check the type & name the of parameter (checkbox in my case, so on & off are the parameter values), one may use the following command to open the model in editable code form.
edit('MyModel.mdl');
and then search for the block name.