Subtleties one's not seen in pests (7)
I believe the answer is:
nuances
'subtleties' is the definition.
('nuance' can be a synonym of 'subtlety')
'one's not seen in pests' is the wordplay.
'one's' becomes 'i's' (Roman numeral).
'not seen in' suggests deleting specific letters.
'pests' becomes 'nuisances' (I've seen this before).
'nuisances' with 'is' taken away is 'NUANCES'.
(Other definitions for nuances that I've seen before include "Subtle distinctions or variations" , "Subtle differences" , "Fine shades (of meaning)" , "'Subtle variations, in meaning perhaps (7)'" , "Suspicion of" .)