Spies taking scoundrel to be an insect (6)
I believe the answer is:
cicada
'insect' is the definition.
(cicada is a kind of insect)
'spies taking scoundrel' is the wordplay.
'spies' becomes 'CIA' (Central Intelligence Agency).
'taking' means one lot of letters goes inside another.
'scoundrel' becomes 'cad' (cad is a kind of scoundrel).
'cia' going around 'cad' is 'CICADA'.
'to be an' is the link.
(Other definitions for cicada that I've seen before include "Droning bug" , "Bug sounding at night" , "Large bug" , "Flier" , "Insect, produces high-pitched drone" .)