Mineral found in first two of six limestone caves (6)
I believe the answer is:
silica
'mineral' is the definition.
(I know that silica is a type of mineral)
I don't understand how the rest of the clue works.
(Other definitions for silica that I've seen before include "Main constituent of sand" , "Compound in quartz" , "Oxide occurring as quartz and used in making glass" , "Common base of rock" , "Quartz used in the manufacture of glass" .)