What are some native Filipino words with very beautiful meaning?

Assuming that what you meant by “native Filipino” is all non-western derived words in all Philippine languages, here are some of the words that I think are beautiful, not only their meaning, but also their sound:

Ragsak- Happiness

Issem- smile

Mutya- a precious stone or gem

Bayani- hero, patriot

Agham- science

Sipnayan- maths

Limbaon- pink

Bughaw- blue

Dayang- darling, princess

Alaga- care/pet. Can be used as euphemism for “parasite”.

Ligaya - joy

Dalisay- pure

Hayag- bright

Kinaiya- inner character

Gigil- cute aggression. On your mind, you want to squeeze or hurt a cute animal or person but it's not like you will really act on it.

Tampo- feeling bad after a loved one or significant other let you down, causing you to avoid them or treat them coldly.

Kalikasan- nature

Oyayi - lullaby

Tala/Bituin- star

Maharlika- a noble warrior or freeman (not a kingdom, the conspiracy theorists destroyed its beautiful meaning)

Karagatan- ocean

Bahaghari- rainbow

Magkaugnay- interconnected

… and many more! Perhaps there are more beautiful words burried in the pages of an unabridged Filipino dictionary waiting to be discovered and used frequently. :)