Investigators found "suspicious circumstances around a possible entry point" at the home, Sgt. Maria Hawke said. She wouldn't comment on whether the entry point was a bedroom window or a door.
Family friend Mary Littlehorn said she heard from others close to the family that a window screen in the girl's bedroom had been knocked down.
Officers kept the block where Isabel lives cordoned off for a second day Sunday, after scores of police and officers from several agencies failed to locate the girl. More than 150 law enforcement officers were involved in the effort, which included a three-mile radius around the home in temperatures that reached the high-90s, police Lt. Fabian Pacheco said late Sunday.
Villasenor said officers had served at least two search warrants. The girl's parents, identified by friends as Becky and Sergio Celis, were helpful in the search for their youngest child, he said.
Villasenor said police had classified the case as a "suspicious disappearance/possible abduction."
"We're not ruling anything out of the investigation at this point because we really need to keep our mind open about all the information that's been brought to us," Villasenor said. "The family has been cooperating with us."
Littlehorn, who joined other family friends at a police command post, said authorities separated the parents Saturday as they questioned them. She said it was difficult for them knowing their daughter was missing.
"She hasn't been allowed to help look for her daughter," Littlehorn said of Becky Celis.
Littlehorn has worked with Becky Celis as a registered nurse in the pediatrics unit at Tucson Medical Center for five years. She said Isabel, whose nickname is Isa, loved to play baseball and dance; the girl was supposed to play in a baseball game Saturday.
"She's just the sweetest, she is feisty, she's full of life and spirit," Littlehorn said.
She said Sergio Celis is a dental hygienist, and that there was no way anyone in the family is involved in the disappearance.
"We all feel this is somebody who's been watching 'Isa' for some amount of time to know where her bedroom is," Littlehorn said.
Investigators were looking into various scenarios, including the possibility that Isabel wandered out of the home she shares with her parents and two brothers. Hawke said Sunday that the wandering off theory was becoming less likely as time passed.
In addition to the highly trained dogs, authorities said they have started checking on the whereabouts of sex offenders in the area as part of standard procedure.
The disappearance has rattled the neighborhood, where volunteers have posted fliers that included a photo of Isabel described as about 4-feet-tall with brown hair and hazel eyes holding up a school achievement award. More than 200 people attended a Sunday evening vigil in an empty parking lot near the family home.
Ron Redondo, whose 14-year-old daughter goes to school with Isabel's older brother, said he wants his kids to not take safety for granted. "We don't know who's out there right now. We don't know if this was a random act or somebody's out there looking for kids."
Erin Cowan, who has worked with Isabel's mom at Tucson Medical Center, brought her 7-year-old daughter. She said it has been on her mind that her daughter is close in age to Isabel.
"I put two-by-fours in their windows this morning," said Cowan, who also has a 12-year-old son. "I guess you can't be too careful, sadly."
At St. Joseph Parish, the Celises and their two sons attended an early Mass Sunday morning, and deacon Leon Mazza described the parents as "very upset."
"We didn't ask for any information. We just let them know if they need help, come see us," Mazza said.
Parish priest Miguel Mariano said the family regularly attends Mass and said he asked the parents if they needed any help from the congregation. "And then they said, 'No, Father, just prayers,'" Mariano said.
The Catholic church and its school are down the street from the family's home, and Mariano said in his sermon that he hoped whoever has Isabel has a change of heart.
"I feel, in the name of the community, we feel we are violated," he said later.