Four deputies went inside and asked a supervisor to tell Ellinger to report to the office, said Cpl. William Parker of the Jefferson County Sheriff's Department.
As Ellinger walked down a hallway, police officers grabbed him and held him against a wall, Parker said.
The deputies said they handled the arrest in that manner because they did not want Ellinger to see them coming and perhaps run.
Ellinger did not resist and was taken to the Jefferson County Sheriff's Department.
Investigators questioned him at length before taking him to the Jefferson County Magistrate's Office where he was arraigned by Magistrate Katherine Santucci.
She reviewed the criminal complaint charging him with one count of abduction, and set bond at $700,000.
He was being held Wednesday at the Eastern Regional Jail east of Martinsburg.
The girl was expected to view a suspect line-up today in an attempt to idenfity her attacker, police said.
The girl's attention to detail helped police in their investigation, police said.
For his Wednesday court appearance, Ellinger wore a black Harley-Davidson cap, a Marlboro T-shirt and blue jeans. A tattoo with blue-black ink was visible on each of his forearms.
He declined to speak to reporters after the hearing.
Berkeley County Sheriff Ron Jones called the case a parent's "nightmare."
The girl went to bed Monday about 9:30 p.m. She was abducted as she, her mother, and her two brothers, ages 4 and 8, slept in the blue, double-wide mobile home. Police would not say where in the house the girl was sleeping.
The sleeping girl was carried from the house trailer and placed in a car. She could not tell authorities what time she was taken from the trailer.
The trailer door had been locked, but the mother told investigators later that it can be forced open if pushed hard enough.
Ellinger was described in court records as an acquaintance of the girl's mother who had been at the trailer before.
The girl did not know Ellinger, court records said.
The girl reported to investigators she was driven by a stranger to a remote section of western Jefferson County, near the Opequon Creek just across from the Berkeley County line, and was sexually assaulted, deputies said.
West Virginia State Police are still investigating that allegation.
The girl's abductor had her get out of the car at the Industrial Park Road about 7 a.m. Tuesday, police said.
A worker found the girl, and her mother and police were called, deputies said.
The mother was asleep and did not know the girl was missing when she was called, deputies said.
On Tuesday, an anonymous caller told deputies that Ellinger might be the man for whom they were looking, according to court records.
On Monday night, Ellinger argued with his girlfriend and left in her car, described in court records as a "tan/goldish," two-door vehicle, which matched the victim's description, according to court records and deputies.
He did not return home until 7:30 a.m. to 8 a.m. Tuesday, court records said.
Lt. K.M. Lemaster and Cpl. J.D. Vanorsdale of the Berkeley County Sheriff's Department went to Ellinger's home and spoke with his mother on Tuesday, according to the court records.
The girl had described her attacker as having a bullet wound scar on his back and a large scar on his chest, according to charging documents.
She also described two tattoos, one on each forearm, according to court records.
The mother told the investigators that her son had been shot when he was a youngster and had a scar on his chest, court records said.
On Wednesday night, deputies with a search warrant raided Ellinger's home and seized several items, deputies said.
Ellinger was described by neighbors as living quietly.
Marie Turner, who lives across the gravel road in the Hidden River subdivision, said she remembers when he was a "good" boy. She said that when he was a child, she watched him and the other children play in the neighborhood.
But over the years he changed, and she seldom saw him any more, Turner said.
The neighborhood is near the Jefferson-Berkeley county line not far from the trailer where the victim had been sleeping.
Ellinger has been in trouble with the law before in Jefferson County.
On March 16, 1994, he was charged with driving while suspended for driving under the influence, failure to utilize a turn signal, not wearing his seat belt and giving false information to police.