The US-backed Arab-Kurdish alliance confirmed on Friday that Manbij was now "fully" under their control, ending a months-long battle to reclaim the city.
Responding to reports of the human shields, European Union foreign affairs chief Federica Mogherini said in a statement that IS continued to "pose a threat to the people of Syria, Iraq, the region as well as to Europe and beyond".
Nasser Haj Mansour, of the predominantly Kurdish Syria Democratic Forces, said Manbij "is under full control", but added that search operations were continuing to find any extremists who might be hiding in the city.
The Democratic Forces of Syria (DFS), a US-backed alliance led by the Kurdish People's Protection Units and including fighters from Arab and other ethnicities, declared Minbij "liberated" after a campaign of more than two months.
The abductions came as Russian and Syrian jets pounded rebel positions in second city Aleppo, the Syrian Observatory for Human Right said.
The capture of Manbij from IS represents the worst defeat for the extremist group in Syria since July 2015, when it lost the town of Tal Abyad on the border with Turkey. They headed for the town of Jarabulus, along the border with Turkey, which their forces hold.
As more territories were lost to the US -led forces, IS grew so desperate that they were using civilians as human shields.
"As a result we have offered three initiatives to save civilians, and to remove them from the battle zones, the last one was five days ago, but it was rejected by ISIS extremists who have no concern about innocent children and women", the council said. It later released around 270 of them.
The Pentagon said it had received reports that fighters were mixing with civilians to use them as human shields, but added it has not been able to verify the reports.
Mr Darwish said another 2,500 civilians that were being held captive had been saved by the SDP.
Here is a look at the IS group's recent territorial setbacks.
The Manbij offensive began in June, when anti-IS forces advanced toward the city from several fronts with the help of USA -led coalition airstrikes.
The United Nations has said that more than 78,000 people have been displaced since then.
Manbij is important because it lies on a key supply route between the Turkish border and the city of Raqqa, the de facto capital of the IS group's self-styled caliphate. Militants held thousands of civilians and threatened to kill them if SDF fighters and their worldwide backers inched closer to their positions, local reports said. Twelve were killed in Hayyan, a small town 15km (10 miles) north of Aleppo, it said.
The western districts held by Syrian President Bashar al-Assad have not experienced the severe deprivations of areas in the east controlled by rebel forces. The correspondent said people had been out on the streets to stock up on supplies after weeks of shortages caused by a punishing government siege.
ARA News reporters have witnessed several civilians being injured and killed by ISIS mines and snipers, some of them are being treated by the doctors in the Amal hospital in Kobane.
In response, rebels and opposition activists say, Assad's forces have responded with intensified bombings that have struck hospitals and involved munitions containing chlorine gas, a choking agent.