Java heap space memory error after saving a large number of files

Hello,

I am running a batch generation of simulated images in Matlab using the software CERR ( http://www.cerr.info/about.php ). It involves large structure files containing image matrices which are opened, modified and then saved using saveas. The following error appears after running about 200 files: Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: Java heap space

Is there any way of clearing the java memory within my code to free some space? I have already increased the java heap size to maximum in the preferences. Any help will be greatly appreciated!