Tours is the best way to see Nepal’s culturally, Historically and Naturally rich site. There are many site for tour in Nepal.
If you are looking for Historical world heritage sites with Durbar square, Hindu Temple , Buddhist Stupas Kathmandu can be the best place. You can extend with Langtang , Ganeshi Himal Himalayas view , sunrise and sunset view Chandragiri Hill, Nagarkot , Dhulikhel and Namo Buddha.
If you want to Natural site like Gupteswor and Bat Cave, Fewa Lake and Begnas Tal, Bindabasini Temple, Mountain museum etc, you may choose Pokhara. You may includes Sarangkot , World Peace Stupa, Dhampus for Annapurna Himalayas view with sunrise and sunset.
Chitwan National Park is another attraction for Jungle Safari with One Horn Rhino and other animals.
If you are looking for a Buddhist site, you may visit Birth Place of Buddha in Lumbini, Tilaurakot, Ram Gram. You may combine with Tansen with Rani Mahal.
There are many other sites, Gorkha Palace, Manakama Temple are Bandipur Hill etc.
In the tour package, you can combined with these site. And it is also possible to combine Nepal, Tibet, Bhutan tour in a package.