Well if I understood you correctly you want to make custom folders to the Application Menu without ApMeFo? Sure, that is possible and that is how I've done, it was mentioned on my previous post. See here: Post #107 on "Making folders and managing icons".
<!DOCTYPE Menu PUBLIC "-//freedesktop//DTD Menu 1.0//EN" "http://www.freedesktop.org/standards/menu-spec/menu-1.0.dtd"> <Menu> <Name>Main</Name> <!-- Search only in the hildon directory. --> <AppDir>/usr/share/applications/hildon</AppDir> <AppDir>/home/user/.local/share/applications/hildon</AppDir> <DirectoryDir>/usr/share/applications/hildon</DirectoryDir> <DirectoryDir>/home/user/.local/share/applications/hildon</DirectoryDir> <OnlyUnallocated/> <Include> <Filename>browser.desktop</Filename> <Filename>mediaplayer.desktop</Filename> <Filename>calendar.desktop</Filename> <Filename>image-viewer.desktop</Filename> <Filename>osso-addressbook.desktop</Filename> <Filename>rtcom-call-ui.desktop</Filename> <Filename>nokia-maps.desktop</Filename> <Filename>camera-ui.desktop</Filename> <Filename>modest.desktop</Filename> <Filename>rtcom-messaging-ui.desktop</Filename> </Include> <MergeDir>submenus</MergeDir> <Layout> <Filename>browser.desktop</Filename> <Filename>mediaplayer.desktop</Filename> <Filename>calendar.desktop</Filename> <Filename>image-viewer.desktop</Filename> <Filename>osso-addressbook.desktop</Filename> <Filename>rtcom-call-ui.desktop</Filename> <Filename>nokia-maps.desktop</Filename> <Filename>camera-ui.desktop</Filename> <Filename>modest.desktop</Filename> <Filename>rtcom-messaging-ui.desktop</Filename> <Merge type="all"/> </Layout> </Menu>