The incident took place at Junior High School 190 in the Queens neighborhood in Feb 2010.
Lawyers for Alexa Gonzalez claim police used excessive force and violation of her rights.
Gonzalez's mother said her child merely scribbled "I love my friends Abby and Faith" in washable green ink on her desk but her teacher dragged her to the dean's office.
Police were called and officers cuffed and arrested the pre-teen. At the police station she was handcuffed to a pole for more than two hours.
"I made two little doodles... It could be easily erased. To put handcuffs on me is unnecessary," the girl said.
City officials have admitted that the arrest was a mistake and said better judgment should have been used by the arresting officers.