There was a separate procedure prescribed under Central Excise Act/ Rules for export to Nepal vide notification No. 20/2004. On December 5, 2011 the Central Government rescinds the notification No. 20/004 with effect form 01/03/2012. So now Export to Nepal is covered with Notification No. 19/2004, that means similar process to other countries except Bhutan.
Now you can export with payment of duty and claim reabte under Rule 18 to export to Nepal or you can export without payment of duty under Rule 19 (Bond/ LUT).