State Sen. Vincent J. Fumo surrendered to the FBI yesterday, submitted to a digital mug shot and fingerprints, then strode into a crowded federal courtroom to plead not guilty to 139 felony charges.

For some time, Fumo had known this day was coming: TV cameras trailing him into the federal complex, an unpleasant FBI visit, an initial court appearance, registration with U.S. marshals.

And yet, as yesterday's surrender experience entered its third hour, a senator accustomed to running things his way found himself at the beck and call of others.

At one point, as his lawyer Richard A. Sprague fiddled with a BlackBerry in the hallway, Fumo said: "I never thought it would take this long."

Fumo did not sound irritated. Just surprised.

The Philadelphia Democrat, accused of using Senate staff and a local charity for personal and political benefit, didn't say much more publicly. Sprague intends to convene a news conference today to address the charges.

Fumo was permitted the courtesy of being the first of a handful of defendants to be arraigned during regular magistrate court yesterday.

The session took five minutes, much of it spent by a clerk, Ryan Watts, reading a lengthy list of the charges.

"Sen. Fumo," Watts said. "Please stand."

Flanked by Sprague and cocounsel Mark B. Sheppard, the senator rose from the defense table, clasped his hands together, and looked the clerk in the eye.

"Vincent Fumo," the clerk continued, "you have been charged with criminal indictment No. 06-319-3 with two counts of conspiracy to commit wire and mail fraud, with one count of conspiracy to defraud the United States, with one count of conspiracy to obstruct justice, with 60 counts of mail fraud, with 41 counts of wire fraud, with nine counts of obstruction of justice, with two counts of obstruction of justice, with 21 counts of obstruction of justice, and with aiding and abetting the filing of a false tax return, two counts.

"How say you to this indictment and the charges in this indictment?"

Fumo didn't pause. "Not guilty."

U.S. Magistrate Judge Thomas J. Rueter ordered Fumo released on a personal recognizance bond and told him to turn over his passport.

The senator, who owns a farm near Harrisburg and a beach home in Margate, N.J., must live in his 33-room home in Philadelphia. His travel is restricted to Pennsylvania, New Jersey, Florida, Delaware and Manhattan.

Like all people charged with federal crimes, Fumo must surrender any guns he owns. In this regard, Fumo is not a typical defendant. A gun collector who has a shooting range in the basement of his home, he owns more than 200 firearms, including machine guns, according to prosecutors.

Assistant U.S. Attorney John J. Pease said Fumo's weapons would be stored in vaults controlled by two firearms dealers. A court official will maintain the keys to the vaults, the prosecutor said.

The grand jury indictment returned Tuesday alleges that Fumo exploited three entities for his personal and political use: his Senate budget and power; the South Philadelphia charity he helped fund, Citizens' Alliance for Better Neighborhoods; and the Independence Seaport Museum.

The indictment charges that Fumo used taxpayer and charity money to pay for political polls, power tools, cars, farm equipment, personal errands, shopping sprees and more. In all, prosecutors say, Fumo misused $2 million.

The indictment also includes the sensational allegation that Fumo hired private detectives to tail ex-girlfriends and dig up dirt on political rivals - including Ed Rendell when he was running for governor.

In addition, Fumo is accused of directing two Senate computer technicians, Leonard Luchko and Mark Eister, to delete e-mail to thwart the FBI and IRS. Last year, Luchko and Eister pleaded not guilty to obstruction-of-justice charges.

The fourth defendant in the case is Ruth Arnao, a former Senate aide and Citizens' Alliance executive director. She appeared in court yesterday with her husband, Mitch Rubin, and lawyer Ed Jacobs, and pleaded not guilty.

Afterward, Jacobs declined to comment.

"Mum's the word," he said.

The trial, before U.S. District Judge William Yohn, is not expected to begin before fall.

Fumo has been indicted twice before, once in 1973 on charges of voter intimidation and once in 1980 for allegedly putting "ghost employees" on the state payroll. He ultimately prevailed each time.

If he is convicted this time, the potential penalties are stiff. He would face at least two or three years in prison, possibly as many as 10.

Contact staff writer John Shiffman at 215-854-2658 or jshiffman@phillynews.com.

Inquirer staff writer Emilie Lounsberry contributed to this article, which contains information from the Associated Press.