If you're sure you're never going to use a module anymore, you can uninstall it to remove it from the system. Also, if you wish to completely remove a module's settings in order to reset it, you'll need to uninstall it (and reinstall it afterwards).
To uninstall a module, click on the "Manage installed LOVD modules" link in the Setup area, and select the module you wish to uninstall. Then, select the "Uninstall module" link.
To reinstall the module, see installing modules.