Footage circulating online showed hundreds of troops outside the headquarters, and an officer is heard saying they came to "clean" the area.
The dissolution of Bashir's National Congress Party, with its top leaders brought to justice - including the ousted president.
On Monday the military council said it was restructuring the joint forces command, appointing a new chief of staff for the army and a deputy.
Fearing that the core of the old establishment is far from gone, the Sudanese Professionals Association (SPA) on Monday reiterated its call for the military council to be dissolved and substituted by a civilian one that will only include "limited" army representation.
"We hope that everyone will head immediately to the areas of the sit-in to protect your revolution and your accomplishments", the SPA said.
The re-instatement of the country's 2005 constitution, which the military council suspended shortly after ousting Bashir.
Earlier the military council met with political parties and urged them to agree on an "independent figure" to be prime minister, an AFP correspondent present at the meeting said.
"We want to set up a civilian state based on freedom, justice and democracy", a council member, Lt. Gen. Yasser Al-Ata, told members of several political parties.
The foreign ministry urged the global community to back the military council "to achieve the Sudanese goal of democratic transition".
Below are their key demands, which the umbrella group Alliance for Freedom and Change says must to be met for the sit-in to end.
"It is time for the transitional military council and all other parties to enter into an inclusive dialogue to effect a transition to civilian rule", they said.
Himeidti is the head of Sudan's Rapid Support Forces (RSF), a paramilitary anti-insurgency force with its origins in the Janjaweed militias of the Darfur conflict. He was once seen as the most powerful person in the country after Bashir and protesters held him responsible for the killing of demonstrators demanding an end to military rule.
The foreign ministry said the military council's chief General Abdel Fattah al-Burhan was "committed to having a complete civilian government" and urged other nations to back the council in order to achieve "the Sudanese goal of democratic transition".