That has happened to Abdulla Darrat, an urban planner from Queens who said he was flagged for extra scrutiny all eight times he flew since June. When he tries to check in online, a message tells him to check in at the airport, where he receives a boarding pass marked with “SSSS” indicating that he must undergo enhanced screening. His name has been handwritten on a card at the podium where an agent checks passengers’ identification, he said.

“They pat me down,” Mr. Darrat, 31, said. “Then they pull out every single article of clothing in my bag. They take out every shirt and every pair of pants.”

After the checkpoint search, which includes swabbing his luggage to check for explosive residue, he said he was often stopped at the gate before being allowed to fly. He said he assumed that the extra scrutiny was because he had flown to Libya to visit relatives. He also expressed support for protests against Muammar el-Qaddafi in 2011, but the extra scrutiny did not happen until this summer.

“It adds this whole air of suspicion about me to everybody on the plane,” he said.