Melbourne's Royal Children's Hospital head of surgery Leo Donnan said it was a "surreal" moment when the girls, who had been joined at the head, were separated at 11am (AEDT) today.

After more two years of planning for the complex surgery, Mr Donnan said his team of 16 doctors and nurses found it amazing to finally see the girls as two separate children.

Plastic surgeons have now moved in to work on the girls, aged two years and 11 months.

Krishna and Trishna will remain in the hospital's intensive care unit for "a number of days", Mr Donnan said.

"And then they'll be slowly woken up."

Mr Donnan praised his doctors, who he said had worked seamlessly to separate the girls.

"This is a once-in-a-lifetime operation that teams would do," Mr Donnan told reporters outside the hospital.

"There really still is a long way to go.

"The girls have a very difficult time ahead of them.

"For the hospital, it is an historic moment and for the girls, an even more historic moment."

The operation went for longer than would have been expected, Mr Donnan said.

He said the staff in the operating theatre had taken planned breaks and the twins were well nourished before the operation.

The mood inside the operating theatre had changed following the separation, Mr Donnan said.

"It's been a very nice stage to move into," he said with a smile.

Shortly after their birth on December 22, 2006, their mother placed the twins in a Dhaka orphanage where two Australian volunteers, Danielle Noble and Natalie Silcock, realised the severity of their plight.

Ms Noble and Ms Silcock began fundraising and, along with Atom Rahman from the Children First Foundation, took the first steps to bring the sisters to Melbourne.

Margaret Smith from the Children First Foundation was trying to contain her joy at the separation of the twins.