What is the best practice to unset session variable in codeigniter?

Don't think an unqualified "best" can be determined.

If you look at the source code for unset_userdata you will see it calls unset($_SESSION['some_variable']);

The advantage to unset_userdata is that you can provide an array of sessions keys to be removed all at once without any further work on your part. In general I'll call unset on $_SESSION if a single item is being removed.

Thank you very much for your kind reply.