I know that when the Athenians were captured after the siege of Syracuse they were held in some quarries where alot of them died. That was rather earlier though.
The Athenians did the same with some prisoners as well.

I can’t think of any good source for the Hellenistic Era but there is good data for Athens in the 5th and 4th centuries…

The Athenians provide one of the best examples of what the period (well technically a bit earlier) might have for prisons – right in agora they had at least one moderately sized building that would seem to have been a prison.

Imprisonment has a formal punishment was limited by the simple fact that it was expensive compared to exile which achieved the same ends and cost the state nothing (or the similar recourse to public humiliation in stocks). Imprisonment did eventually become an alternative punishment for prisoners who could not pay a fine they would otherwise have been administered. By the 4th century imprisonment emerged a fairly standard alternative punishment to a fine – a sort of democratic innovation since it did favor the rich as fines did.

For a good discussion of prison life in Athens (but conservative on the question of Imprisonment as a penalty) –

‘The Prison of Athens: A Comparative Perspective’ V Hunter, Phoenix 51 pp 296-326.

For a more assertive view that Prison could be a punishment in itself and some references to other Greek states and Rome –

‘Imprisonment in Classical Athens’ D. Allen CQ 47 121-135