During the wave of protests last week that led to Morsi's removal, Brotherhood supporters used guns in several instances to defend their offices when opponents marched on them — or outright attacked them.
Pushing ahead with the military "road map" is likely to further infuriate Islamists who have vowed to continue protests until Morsi is restored and now depict the military as willing to wipe them out by force of arms.
Outside hospitals and clinics near Monday's violence, Morsi supporters waved the bloodied shirts of the dead or wounded.
"The only thing the military understands is force and they are trying to force people into submission," said Marwan Mosaad, speaking at a field hospital run by Morsi's supporters. "It is a struggle of wills and no one can predict anything."
Abu Ubaida Mahmoud of Al-Azhar University said he had been praying when the sit-in's security teams began banging on metal barricades in warning. He then saw troops coming out of the Guard complex.
"The number of troops that came from inside was stunning," said Mahmoud, who was wounded in the hand.
It was "as if they were firing at an enemy," said another protester, Ahmed Youssef.
By the afternoon, the sit-in site was cleared along with blockades that had been set up on roads. The site of the early morning clashes, a strip of road about a kilometer long (about half a mile), was covered with rocks, shattered glass, shoes, clothes, prayer rugs and personal photographs.
A big Morsi banner remained hoisted in front of the Republican Guards' building. On the ground below it, graffiti read: "Where are our votes?"
Associated Press correspondent Paul Schemm contributed to this report.
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