Often: rape, torture kill, or enslave.
In other cases where there was a negotiated surrender, the terms of the surrender dictated what happened to the populace. It might, for example, be that they had to pay an indemnity based on their ability to pay, that they had to pay ongoing tribute, or cede land which might be used for resettlement of retiring legionnaires. Yet again, the Roman commander, having received their surrender had, under the Roman patron-client system, obligations to the conquered people. He had to negotiate with the Senate the best terms for them - when they surrendered to him, they became his clients, and he their patron. It was often in his own interests to do as well as he possibly could, as they were then obligated as clients to support him in future. Pompey's strength, for example, lay in the obligation of the cities and tributary kings in the east and the tribes in Spain, who were obligated to him personally after he conquered them and arranged a settlement of their affairs.
The other factor was that Rome wanted to establish stability in its growing empire and especially on its frontiers, and generally gave lenient conditions and reinforced local government. After the fighting was over, the move was to settle the problem, not to unnecessarily alienate the populace and aristocracy, so the rape/torture/slaughter option was for extreme cases of revolt or prolonged resistance, where it was felt that an example had to be made.
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