NEW YORK (CBSNewYork) —  Allen Weisselberg, the Trump Organization’s chief financial officer, and lawyers for the company appeared in front of a Manhattan judge Thursday and pleaded not guilty to charges in what prosecutors called a sweeping tax fraud scheme.

The charges were unsealed after former President Donald Trump’s longtime aide and the company were indicted by the Manhattan District Attorney and Attorney General Letitia James, CBS2’s Alice Gainer reported.

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CBS2’s cameras captured the moment Weisselberg, 73, arrived at Manhattan Criminal Court almost an hour earlier than planned.

Manhattan DA Cy Vance Jr. was also seen heading into court after leading the two-year investigation.

Weisselberg entered the courtroom in handcuffs and entered the not guilty plea on charges related to alleged failure to pay taxes on corporate benefits and perks. He said nothing while leaving the courthouse.

Moments before Weisselberg pleaded not guilty to grand larceny, lawyers on behalf of the Trump Organization pleaded not guilty to charges of scheme to defraud.

The 15-count indictment alleges Weisselberg and the Trump Organization cheated New York State and New York City out of taxes by conspiring to pay senior executives off the books from 2005 through this year.

Prosecutors allege Weisselberg evaded taxes on $1.7 million in income that included apartment rent, car payments and school tuition.

“It is a corporate apartment, it is a corporate car,” said Trump Organization attorney Alan Futerfas. “The payment of his grandchildren’s tuition, which every expert on the planet will tell you, is a gift.”

“The indictment speaks for itself,” AG James said.

Weisselberg’s estranged, former daughter-in-law turned over several boxes of documents from her divorce to prosecutors. She claimed they show financial transactions from Weisselberg to her family for rent, cars and private school tuition.

“The tax issues, tax evasion, the tax fraud became apparent,” Jennifer Weisselberg told CNN.

“He lives in a bubble where he believes everything Trump says,” she also said.

Weisselberg, an employee of 48 years, operated as CFO of the Trump Organization as well as the Trump family’s personal bookkeeper. He appeared on Trump’s reality show “The Apprentice.”

Watch Alice Gainer’s Report

Although the former president was not charged, these allegations raise questions about his knowledge of or involvement in suspected illegal business practices.

On “CBS This Morning,” Barbara Res, who was an executive vice president at the Trump Organization, said, “Nobody does anything major without Trump’s knowledge and usually approval.”

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The former president released a statement saying, “The political Witch Hunt by the Radical Left Democrats, with New York now taking over the assignment, continues. It is dividing our country like never before!”

“They come after me, New York radical left prosecutors come after me. You gotta always fight. You gotta keep fighting. It’s a disgusting thing. It’s very unfair,” Trump said.

“If the name of the company was something else, I don’t think these charges would’ve been brought,” Futerfas said.

Trump called Weisselberg an honorable man who has been with him for decades.

Prosecutor Carey Dunne said the case is not about politics.

He told the court, “Politics has no role in the jury chamber and I can assure your honor it played no role here.”

Watch John Dias’s Report

While Weisselberg pleaded not guilty, the big question is, what if he flips?

Former Trump attorney Michael Cohen says Trump has plenty to worry about.

“Everything went through Donald,” Cohen said. “Whether it was the acquisition of paper clips, light bulbs, furniture … Everything would have a Donald Trump signature on it.”

Now, Weisselberg has a possible decades-long prison sentence hanging over his head.

“This is a man in his 70s. If he looks at Michael Cohen and look what happened to him in terms of imprisonment, when they put the cuffs on you, as they did today at the courthouse, you may have quite a change of mindset,” CBS Legal analyst Rikki Kleiman said.

Trump is not expected to face charges, but he isn’t in the clear. The grand jury is sitting until November, so it’s possible he could see indictments.

The former president said his company’s actions were “standard practice” and “in no way a crime.”

Weisselberg was released on his own recognizance and surrendered his passport because prosecutors considered him a flight risk. His next court date is in September.

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CBS2’s John Dias and Dick Brennan contributed to this report.

Alice Gainer