Set aside organ, one of two not in pristine condition (9)
I believe the answer is:
earmarked
'set aside' is the definition.
(I've seen this before)
'organ one of two not in pristine condition' is the wordplay.
'organ one of two' becomes 'ear' (one of two ears).
'not in pristine condition' becomes 'marked' (something marked is not pristine).
'ear'+'marked'='EARMARKED'
(Other definitions for earmarked that I've seen before include "Reserved, set aside" , "Put by for later" , "Carefully chosen" , "Set aside for a specific purpose" , "appearance of one who underwent piercing?" .)