Dozens of relatives of the victims watched from nearby as workers from a port in Mokpo conducted operations to dock the heavy lift transport vessel that carried the 6,800-ton Sewol, lying with its rusty blue bottom facing land.
Finding the remains of the missing victims would bring a measure of closure to one of the country's deadliest disasters.
Most of the 304 people who died when the Sewol sank on April 16, 2014, were teenagers on a school trip, triggering a national outpouring of grief and outrage over what were seen as poor government rescue efforts. The anger contributed to the ouster of President Park Geun-hye, who was arrested earlier Friday over allegations of corruption.
"He was in the dark and frightening deep seas for three years, but he's now going to Mokpo," Yoo Baek-hyeong, the wife of a missing teacher, told reporters on a patrol boat where they watched the transport vessel depart for port.
"I want to find even just a piece of his hair. He would have been wearing his wedding ring ... I want to find all of those things," she said.
Salvage crews on two barges raised the Sewol last week, rolling up nearly 70 cables connected to metal beams divers had installed beneath the ferry, which was lying on its left side below 44 meters (144 feet) of water.
The vessel was welded in place on the transport vessel to maintain balance during the trip, and disconnecting it will take several days. It will be further emptied of water and fuel, then moved to a dry dock where workers are expected to spend weeks cleaning it and evaluating it for safety.
Investigators will then begin searching for victims' remains and for clues that could further explain the cause of the sinking, which has been blamed on excessive cargo, improper storage and other negligence.
"We hope to move the ferry to the dry dock around April 6," Lee Cheoljo, an official from the Ministry of Oceans and Fisheries, told reporters. "We cannot say for sure when we will be able to start the searches, but we will try to start them as early as we can."
According to the oceans ministry, the searches will be conducted by a team of 100 government investigators, including experts from the National Forensic Service. An eight-member civilian panel was formed to monitor their efforts.
There are disagreements over how to proceed with the searches, which could take months.
Government officials favor cutting off the ferry's passenger cabin areas and raising them upright before searching for the missing victims, which they say would improve efficiency and also be safer for the investigators. Families fear that cutting into the ship might harm any victims' remains.
Lee said the government will further discuss search methods with the relatives.
"The priority is to secure a safe entrance into Sewol's wreckage for investigators," Lee said. "There are passenger cabins where the remains of the victims are presumed to be and we plan to search those spots first."
Of the 476 people on board the stricken ferry - mostly teenagers on a school outing - just 172 survived. A total of 295 bodies were recovered.
The ferry was found to have been overloaded with cargo. A large investigation team including forensic experts are due to inspect the wreck in the coming weeks for further clues as to why it sank.