Waste very long time in underground prison (7)
I believe the answer is:
dungeon
'underground prison' is the definition.
(I've seen this before)
'waste very long time' is the wordplay.
'waste' becomes 'dung' (dung is a kind of waste).
'very long time' becomes 'eon' (an extremely long period of time).
'dung'+'eon'='DUNGEON'
'in' is the link.
(Other definitions for dungeon that I've seen before include "Prison cell, often underground" , "Unpleasant cell" , "Eg, the Black Hole of Calcutta" , "Place of confinement underground" , "prison the result" .)