Waste millions of years in an underground cell (7)
I believe the answer is:
dungeon
'an underground cell' is the definition.
(I've seen this before)
'waste millions of years' is the wordplay.
'waste' becomes 'dung' (dung is a kind of waste).
'millions of years' becomes 'eon' (I've seen this in another clue).
'dung'+'eon'='DUNGEON'
'in' acts as a link.
(Other definitions for dungeon that I've seen before include "Unpleasant cell" , "prison the result" , "Dark underground cell for prisoners" , "old prison" , "Keep" .)