Stone and tree over den, one hidden (6)
I believe the answer is:
ashlar
'stone' is the definition.
(I know that ashlar is a type of stone)
'tree over den one hidden' is the wordplay.
'tree over' becomes 'ash' (ash is a kind of tree. I am not sure about the 'over' bit.).
'den' becomes 'lair' (synonyms).
'one' becomes 'i' (Roman numeral).
'hidden' is a deletion indicator.
'lair' with 'i' taken out is 'lar'.
'ash'+'lar'='ASHLAR'
'and' acts as a link.
(Other definitions for ashlar that I've seen before include "Rectangular block of cut stone" , "Building block" , "Stone used in building" , "Dressed stone block" , "building material" .)