But while the man was being held, FBI agents approached the squad car, and police ordered the man back out of the car. FBI agents questioned him -- still fully undressed -- on the sidewalk.
In an early phase of the lock down, a man could be seen lying face down on the street with his hands outstretched in front of him and his legs crossed. It is unclear whether this was the man who was arrested and ordered to undress.
Explosives once more
Police requested that people in the lockdown area turn off their cell phones. Authorities suspect cell phones were used to detonate the bombs that flung metal through the crowds at the marathon Monday.
Dozens of police from various units arrived in Watertown, some in SWAT uniforms, others wearing helmets. Large crowds gathered around a trove of emergency vehicles that had congregated in the neighborhood, WCVB reported.
Homeland Security Investigations deployed agents to the scene, a Homeland Security spokesman told CNN.
Police also said they were going door-to-door, street by street, searching the Watertown area.
Area residents have been on edge after two bombs ripped through the crowd near the finish line of the Boston Marathon, killing three people and injuring 178 others.
Federal, state and local agencies are still investigating the marathon bombing.
Police, who were seeking two suspects in the attack, now believe they have found them.
CNN's Terence Burke, Dave Alsup, Carma Hassan, Jake Tapper, Drew Griffin, Steve Almasy and Chandler Friedman contributed to this report.