How to customize (add/remove folders/directories) the "Places" menu of Ubuntu 13.04 "Files" application?

First of all, open a nautilus window to the directory you wish to add. Then click the small cog icon in the top right of the nautilus window and click the 'Bookmark this location' entry. It will be added to the "Bookmarks" section of the sidebar.

I met the same problem and I found the following solution:

gedit ~/.config/user-dirs.dirs

remove the list you do not want. However, once you login again, it will reset, so -->

echo "enabled=false" > ~/.config/user-dirs.conf

Reference: http://jamesmcminn.com/2012/12/removing-entries-from-nautilus-3-6-places/

Alternatively, one may also solve everything by directly modifying Sysadmins file in /etc/xdg/user-dirs.conf, for more details refer to: Functions of xdg-user-dirs