Matlab still busy after script is finished.

I am running a lot of huge simulation using simulink and Matlab. But everytime the script is done(I am sure it's done bacause the last line of the script is executed), matlab will keep busy for a long time which depends on how many simulation I've run.

The script will call a function, which will have a simulink model to run, for many times. During and after each function call, a lot of data will be assigned to 'base' workspace using 'assignin' and the simulation is also run in base using 'evalin'. I am wondering if this is the reason.