Mass transportation to and from the Boston area is virtually shut down Friday morning, with the exception of airplanes, which continue to take off and land at Logan International Airport.

Train and bus service is shut down as police conduct a massive manhunt for one of two suspects in Monday’s Boston Marathon bombing. People waiting at bus and subway stops were told to go home.

Amtrak has stopped trains about an hour south of the city in Providence, R.I. Amtrak has also suspended its entire Downeaster service, which runs from Brunswick, Maine to Boston, according to spokesman Cliff Cole.

The Massachusetts Bay Transportation Authority, which operates commuter trains into Boston as well as the city’s subway — called the T — and the city’s buses suspended all operations. The one exception appears to be the Silver Line bus between Logan and downtown.

All major highways remained open, according to the Massachusetts Bay Transportation Authority. The exception is Watertown, the center of the manhunt.

Megabus has canceled at least 18 buses between Boston and New York, New Haven, Conn., Hartford, Conn., Burlington, Vt. and Philadelphia. More than 1,000 passengers were affected, according to spokesman Mike Alvich. They received emails offering a refund or the option to rebook for free.

Bolt Bus, Greyhound and Peter Pan Bus Lines have all also suspended service. Passengers booked on canceled Bolt trips have already received refunds to their credit cards, according to Timothy Stokes, spokesman for Greyhound and Bolt Bus.

Logan airport remains open, although getting there will be a challenge for many passengers. On a typical day, the airport has about 1,000 flights, according to flight tracking site FlightAware.

JetBlue, the largest airline in Boston with about 100 daily flights, is allowing anybody scheduled to fly to or from Boston to change their ticket for free. Delta — which has about 70 daily Boston departures — also hasn’t canceled any flights in Boston. Spokesman Morgan Durrant says the airline expects on-time departures and is considering extending a travel waiver issued earlier in the week.

American Airlines hasn’t canceled any of its 31 daily flights in Boston. The airline is allowing passengers scheduled to fly today to rebook onto flights Saturday or Sunday without penalty, according to spokeswoman Andrea Huguely.

The Federal Aviation Administration imposed an air traffic restriction on the Boston area “to provide a safe environment for law enforcement activities.” It bars flights below 3,000 feet in a radius of 3.5 miles around the manhunt area. Such restrictions have minimal impact on commercial flights in the area.

James Kearney, an information technology consultant from East Amwell, N.J. was in town for business and managed to make it out on a United flight at 10 a.m. He said via email that the 15-mile trip from the Marriott in the western suburb of Newton to Logan on the Massachusetts Turnpike “was extremely quiet during rush hour.”

Once at the airport, he said, the situation was “pretty standard.”

“Even security was fast and uneventful,” Kearney wrote.

Colin Alsheimer, who was on a flight from Dallas to Boston Friday morning, said that the manhunt dominated conversations during boarding.

“People were checking for news updates on their phones and talking with their seat neighbors,” Alsheimer wrote in an email from the American Airlines flight.

After landing at 12:15 p.m., Alsheimer said the airport was surprisingly normal.

“People do seem focused on news broadcasts in terminal bars,” he said. “Only saw an increased security presence on the road leading into Logan. Must be focusing more on departures.”

Kacey Brister, a senior at Louisiana State University, was supposed to have an interview for a public relations job in Boston at 3 p.m. Friday. She was flying on Southwest Airlines from New Orleans to Boston via St. Louis.

Before boarding the last leg of her trip, Brister said that everyone was fairly calm at the gate.

“The biggest concern for most people was how they were going to get from Logan to their hotel, home,” she wrote in an email, adding that there was “a sense of camaraderie between passengers.”

Not everyone was so calm, however. “My mother has begged me” to turn around, she said.

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Photo Credit: An MBTA transit official closes a door at Malden Center station in Malden, Mass. Friday, April 18, 2013 as area MBTA commuter trains are suspended. Elise Amendola / AP Photo