You can use MATLAB to check if a particular process is running on the system and make MATLAB wait until this process is closed.
Here is a simple example that uses a DOS function SLEEP as the executable. Attached are two files testRun.m and isprocess.m. You will need the isprocess.m file to check the system processes for a particular exe.
testRun shows a sample:
!sleep 30 &
disp('MATLAB continues after calling EXE')
flag = true;
disp('EXE still running');
flag = isprocess('sleep.exe');
disp('continuing with MATLAB script')