The focus of the operation will be two large shared veins at the back of the conjoined twins heads, which risk being ruptured as doctors attempt to split them between the boys.
If the surgery is successful, the medical team at New Yorks Montefiore Medical Center hope to carry out a fourth operation in May to finally separate the twins.
Carl and Clarence Aguirre arrived in New York City from the Philippines on Sept. 10 last year and underwent a series of tests and examinations to prepare them for the highly risky separation procedure.
Surgical team leader James Goodrich said the sharing of the veins in the boy heads had created a "lake" of blood between their brains.
"Weve decided to give the lake to Clarence," Goodrich said. "What were trying to do is reverse the flow in Carl and try to get his blood to flow into deeper veins."
Conjoined twins occur in approximately one of every 200,000 live births. Twins joined at the head are extremely rare representing roughly one in 10 million live births.
Instead of performing one lengthy operation, the medical team at the Montefiore hospital decided to conduct the separation over the course of as many as four shorter operations.
The first surgery took place last October with a five-hour operation to place balloons underneath the boys scalps in a process called tissue expansion.
The operation on the Filipino twins was requested by their mother Arlene, a registered nurse who expressed her desire to have them separated so they will have an opportunity to lead independent lives.