Several television stations ran footage of what appeared to be pro-Mursi protesters firing automatic rifles at soldiers from behind sandbag barricades.
At a hospital morgue nearby, a Reuters reporter counted 29 bodies, including that of a 12-year-old boy. Most had died of gunshot wounds to the head.
The health ministry put the overall death toll at 95 people, including both police and civilians, with other sources saying at least 17 were killed in Fayoum province and five in Suez.
Mursi supporters besieged and set fire to government buildings and several churches were attacked, state media said.
Mohamed El-Beltagi, a leader of Mursi's Muslim Brotherhood movement that has led the protests, said his 17-year-old daughter had been killed in the clashes.
Nine hours after the start of Wednesday's operation, crowds of protesters were still blocking roads, chanting and waving flags as security forces sought to prevent them from regrouping.
"At 7 a.m. they came. Helicopters from the top and bulldozers from below. They smashed through our walls. Police and soldiers, they fired tear gas at children," said teacher Saleh Abdulaziz, 39, clutching a bleeding wound on his head.
"They continued to fire at protesters even when we begged them to stop."
The move to break up the camps appeared to dash any remaining hopes of bringing the Brotherhood back into the political mainstream, and underlined the impression many Egyptians share that the military is tightening its grip.
The operation also suggested the army had lost patience with persistent protests that were crippling parts of the capital and slowing the political process.
It was the third time since Mursi's ouster six weeks ago that security forces had opened fire on protesters in Cairo, killing dozens of people on each occasion.
so I guess they must calm down..
