He is second-in-command of one of the world's deadliest terror groups, wanted by America for masterminding the 2010 Times Square bomb plot.
The dramatic raid, details of which have only emerged now, was all the more daring because Mehsud was forcibly abducted while heading to a rendezvous with America's allies in Afghanistan's top spy network, the National Intelligence Directorate.
According to briefings from Kabul, Latif Mehsud was a prized asset for Afghanistan's beleaguered spies.
A former driver and personal assistant to Hakimullah Mehsud, TTP's leader, Mehsud has been cultivated as a double agent for the past two years. In recent months he has worked with Afghans even while he was wanted in the US.
The mission to seize the 30-year-old amounted to a breach of trust among allies, and its fallout could affect the future of America's deployment in Afghanistan.
Aimal Faizi, the spokesman for Hamid Karzai, the Afghan president, openly complained about the US tactics. "The Americans forcibly removed him and took him to Bagram," he said. The sensitivity of Mehsud's seizure forced John Kerry, the US secretary of state, to make a lightning dash to Kabul to talk down an incensed Mr Karzai.
Once seen as a hand-picked ally, Mr Karzai has lately morphed into a ferocious critic. In the days following Mehsud's capture, he launched his strongest ever attack on America's record in his country.
"On the security front, the entire Nato exercise was one that caused Afghanistan a lot of suffering, a lot of loss of life, and no gains because the country is not secure," he said.
The timing of his condemnation of the American-led alliance was particularly sensitive. It coincided with the 12th anniversary of the Nato mission to eliminate the Taliban and al-Qaeda in Afghanistan.
Only days later did it become apparent that the source of Mr Karzai's ire was the secret operation to seize Mehsud.
The US State Department has signalled that despite Mr Karzai's fury, Mehsud would remain in their custody and would be treated as an enemy of America.
"Mehsud is a senior commander in TTP, and served as a trusted confident of the group's leader, Hakimullah Mehsud," said Marie Harf, the department's spokesman.
"TTP claimed responsibility, as folks probably know, for the attempted bombing of Times Square in 2010 and has vowed to attack the US homeland again. TTP is also responsible for attacking our diplomats in Pakistan and attacks that have killed countless Pakistani civilians."
After he was whisked away from the convoy of 4x4 vehicles, Mehsud was bundled on to a helicopter for the short flight through the mountain passes to Bagram.
The fastest flight path from the interception to Bagram takes the helicopter over Mr Karzai's presidential palace. Behind the barbed wire of the Bagram compound, Mehsud is undergoing interrogation for information on TTP's latest plots to attack America and its forces.
It was not disclosed if Mehsud was injured in the operation or if there was an exchange of fire between the US and the Afghans during the incident on the high mountain highway that cuts from the capital to the Pakistani border.