Mohammad Iqbal got back to his Shirley home from work about 2:30 a.m. Thursday, at the end of his shift driving a limousine, and was awakened by knocks on the door at 6 a.m.

It was two FBI investigators, flashing their badges. Iqbal, in an interview, said they searched his home and questioned him for more than five hours about whether he was involved in a terrorist plot to detonate a car bomb in Times Square - an incident Iqbal said he had nothing to do with.

"I've got nothing to hide," he said. "They went through everything. You could say they went through my socks."

A Pakistani Muslim from Punjab province who said he moved to America in 1995, Iqbal, 46, said the investigators were especially interested in talking about his connection to Muhammad Younis, a Centereach man who FBI agents also were seen talking to Thursday.

Iqbal said he told the agents he knows Younis - they have been friends for about 15 years - and that he "doesn't see anything" about Younis that could link him to terrorism.

The experience left Iqbal shaken. He said he signed a consent form for a search of his home on Free State Drive on a tree-lined residential street of single- and multifamily homes.

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The investigators' main focus was Younis, he said.

Iqbal told reporters that he has no political agenda and had never heard of accused Times Square car bomber Faisal Shahzad until Shahzad was on the news recently.

He described the FBI search as "calm," although agents took pictures of everything - even the wiring of the house - copied his computer's hard drive and took a cell phone. Agents also found a diary that had Younis' name in it, he said.

The agents asked Iqbal if he recently had sent any money to Pakistan, and he said he doesn't know anybody there.

Iqbal said he and Younis know each other from working together at a 7-Eleven convenience store in East Patchogue in the mid-1990s. They also lived together briefly as roommates, he said.

Iqbal described Younis as "not bad people" and a calming influence.

"I do have an anger problem - you curse me, I'll curse you right back. He'll just walk away," he said.

He said he last spoke with Younis a few days ago, just to say hello.

Iqbal said while he thought the FBI search was fair, he felt targeted because of his Muslim background.

"I feel terrible. I feel like I was treated like a [jerk] in front of my five kids," he said, though he added that "they were just doing their job."

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He said his 5-year-old daughter, who witnessed the search, was terrified by the ordeal. He and his wife have five children, who range in age from 2 1/2 to 9.

"The neighbors, what are they going to think of me now?" he said.

Iqbal said part of the reason he cooperated with the FBI is because "otherwise how will they find these people" who were complicit in the crime.

Iqbal said he believed the FBI was done questioning him after they left. By 7 p.m., he was tired and frustrated that he was going to miss a day of work.

As the sun started to set, the ice cream truck hummed down Free State Drive, and Iqbal treated his children to ice cream bars.

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"I live here with my family," he said. "This is what I care about."

Meanwhile, at the Centereach home where Younis rents an apartment, landlord Ashim Chakraborty told Newsday Younis and his wife had rented a one-bedroom basement apartment from him for around 18 months. FBI agents had searched that apartment Thursday morning, he said.

No one opened the apartment door. But an unidentified woman screamed at reporters form behind a closed door.

"Go away. We're Americans," she yelled. "Go pick on a real terrorist, you morons."

Chakraborty said FBI agents had searched the apartment, as well as a storage shed in the backyard. He said the shed contained only a lawn mower.

He said Younis and his wife, Christina, who is from the United States, have an 11-year-old daughter and pay less than $1,000 a month in rent. Chakraborty said he lives upstairs.

He said Younis attends a mosque in nearby Selden.

Chakraborty told Newsday FBI agents knocked on his door about 7:30 a.m. Thursday and told him they had to collect information. He said they also inspected his tenants' cars.

He said he did not see any evidence being taken nor anyone being arrested.

Several reporters flocked to a mosque in Shirley, acting on a tip that it had been raided. Abdul-Lateef Poulos, imam at the mosque, Masjid Umar Bin Khattaab, arrived to find a herd of media asking him about possible ties to terrorist groups.

Poulos confronted reporters to say he finds it "unfair and inappropriate" to link his mosque to terror activities because of an FBI presence in the neighborhood earlier in the day.

Poulos added that terrorist actions "always have a negative effect on the majority of us who are just living our lives, going to mosque."

It later emerged that the search had taken place elsewhere in Shirley, at an address on Free State Drive that documents show as one of Younis' previous residences.

From his home nearby, neighbor Walter Kulsa, 67, a retired security guard, said he had noticed unmarked SUVs with tinted windows parked near the house of Mohammad Iqbal - a friend of Younis - for at least a week. On Sunday, Kulsa said, he talked to a man in an SUV parked there who showed Kulsa a federal agent's badge.

Kulsa described Iqbal as a quiet neighbor.

"It's spooky, unbelievable" to think of Iqbal being considered in connection with a terror incident, he said.

In Centereach, a woman who lives next door to Younis' home and did not want to give her name said she woke up to the sound of helicopters and thought at first a drug raid was under way in the neighborhood.

"I figured with all the heroin around here . . ." she said. "Then I saw police out there and I asked what was going on. The police wouldn't say, but told me, 'You're not in danger.' "

Authorities searched two residences linked to Muhammad Younis, 43, who his current landlord said is of Pakistani descent and works as a supplier to home-improvement stores. 

Ashim Chakraborty, Younis' landlord in Centereach, answered a knock at his front door at about 7:30 a.m. and found an FBI agent on his stoop.

"He said we have to investigate, and I don't ask" questions, Chakraborty said.

The block was filled with police vehicles - at least 10, he said - and a dozen officers and investigators who examined the storage shed in the backyard and the basement apartment where Younis lives with Kristine Malfi.

How many search warrants were executed in the Northeast - and all of their locations - remains unclear. Raids took place in Maine, Massachusetts and New Jersey in addition to those on Long Island.

FBI Special Agent Gail Marcinkiewicz told Newsday the searches resulted from information gathered in the investigation of Shahzad.

U.S. Immigration and Customs Enforcement spokesman Brian Hale told The Associated Press three people were arrested on suspected immigration violations: two in the Boston area and one in Maine.

The arrests are administrative and not criminal, he said.

Shahzad, 30, a Pakistani-born U.S. citizen, is alleged to have driven a bomb-laden Nissan Pathfinder into Times Square on May 1, leaving the vehicle parked near the intersection of Seventh Avenue and 45th Street in hopes of creating a massive explosion.

On Long Island, FBI officials confirmed the raids were in Shirley and Centereach. Suffolk police spokesman Timothy Motz told Newsday: "We are providing personnel to support the FBI in an ongoing operation."

With John Valenti, Tom Brune and Reid J. Epstein