The first steps in the Islamization of the Egyptian government will happen Monday and Tuesday when Egyptians go to the polls to elect a parliament - the first of several scheduled votes over the next few months.
Meanwhile, protestors in Tahrir Square continue to demonstrate against military rule, calling on a transfer of power to civilian authorities immediately.
But the demonstrators gathered in Cairo's Tahrir Square want the council to make way for a civilian interim administration immediately. They reject its promise to complete the handover by July and its choice of 78-year-old Kamal Ganzouri to form the next cabinet.
Activists had called for a mass rally to pile pressure on the generals, and by mid-afternoon there were thousands in the square, hub of the unrest that toppled Mubarak.
Field Marshal Mohamed Hussein Tantawi, head of the council, said the army would ensure security at the polling booths.
"We are at a crossroads. There are only two routes, the success of elections leading Egypt toward safety or facing dangerous hurdles that we in the armed forces, as part of the Egyptian people, will not allow," he declared.
Abdel Moneim Aboul Futuh, an Islamist presidential candidate who opposes military rule, said: "The nation is larger than Field Marshal Tantawi and Lieutenant General Sami Enan and the military council. A government with revolutionary leadership must be formed to meet the demands of Tahrir Square."
State television quoted Tantawi as saying the army's role in the new constitution would be unchanged: to protect the nation.
The refusal of the army to relenquish power even after the elections is going to be a source of constant friction between reformers and the military. But it appears that many Egyptians - perhaps a majority - are tired of the chaos and want some semblance of law and order so that the economy, which is near collapse, can recover.
The Muslim Brotherhood won't win a majority. But they will be the largest political party by far and should have little difficulty in forming a government with other like-minded parties. It will be then that many in the west may wish that the military maintains some kind of role in order to influence and temper what comes out of the new government.