[status, result] = system('EX.exe');

[status, result] = system('start EX.exe');

setappdata(0, 'running', 1);

tim = timer(...
    'StartDelay', 2, ...
    'TimerFcn',   'while getappdata(0, ''running''), fprintf(''timer running ...n''); pause(1); end' ...
);

fprintf('Starting timer.n');
start(tim);

fprintf('Calling external program ...n');
[s,r] = system('EX.exe');
fprintf('External program returned %d.n', s); % <-- This is never reached.

setappdata(0, 'running', 0);

fprintf('Stopping timer.n');
stop(tim);
delete(tim);

>> runtime = java.lang.Runtime.getRuntime();
>> process = runtime.exec('program arg1 arg2');
>> ...
>>
>>   % when you want to collect results.
>> process.waitFor(); % block until program returns.
>> process.exitValue(); % fetch process return code.
>>
>>   % or, if you need to abandon the work,
>> process.destroy(); % violently kill process