Basically, you have to do a backup of the master to have the PHP code and that you will restore somewhere else.
Once you have restored the master, you can uninstall JMS to get a standalone Joomla.
When done, you can copy all the specific files and folders of your slave site into the new location.
Such kind of operation can be done with a linux tar command.
See the FAQ for the backup / restore.
www.jms2win.com/en/faq/faq-joomla-multi-sites#cat-268
tar -chzf [Deploy Dir].tgr [Deploy Dir]
If you do this command in the slave site deploy directory, you will get both master and slave site files merged together.
Once you have that, you have to make a backup of you DB to be able restore it into the new standalone location