Inside the city, positions that had long been manned by fighters of the Kurdish-Arab Syrian Democratic Forces (SDF) were abandoned, though some remained in the central Al-Naim square, dancing and ululating as they celebrated their victory.
The SDF battled for more than four months, with US-led coalition support, to capture the city that was once the de facto Syrian capital of IS's self-styled "caliphate".
They announced the end of combat on Tuesday, though operations to clear explosives and seek out sleeper cells were ongoing.
"Some of the forces withdrew, others will remain in the city until we finish the minor combing operations, then the city will be handed over to the civil council," said SDF commander Rojda Felat yesterday.
"After the end of military operations, a large part of the forces have moved out of Raqa to other areas, including Deir Ezzor," added Mustefa Bali, spokesman for the Kurdish People's Protection Units (YPG), the main component of the SDF.
"SDF intelligence is investigating them, including a number of foreigners," he told AFP.
The city's capture Tuesday came after the SDF seized IS's last two main positions, the municipal stadium and national hospital, in quick succession.
Both sites have been heavily mined and remain to be cleared, SDF commanders said.
"There are bodies inside the hospital itself that we haven't yet removed because of the mines," said commander Clara Raqa.
The official handover is expected to come as early as today, but the body has already spent months working on reconstruction plans.
They will inherit responsibility for a ghost town that lacks basic services and infrastructure.
On the city's streets yesterday, blankets that had been hung in front of windows to shield residents from the view of snipers fluttered in the wind, but there was no movement otherwise.
A few scrawny cats and dogs picked their way over the rubble that is strewn across the city, up to 80 per cent of which was described as uninhabitable by the UN last month.
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