Dhaka Metropolitan Magistrate Saiful Islam framed charges against them in the case on Wednesday.
However, Shafiqur Rahman and Golam Parwar, now in jail, and 78 others, who are on bail, pleaded not guilty to the charges.
The magistrate issued arrest warrants against eighteen other accused who have been on the run since the case was filed.
September 17 has been fixed for starting trial of the case.
According to the case statement, a group of 200-300 leaders and activists of Jamaat-Shibir, led by Golam Parwar, vandalised several vehicles and torched two motorbikes in Motijheel on November 5 of 2012 to protest the arrest of their central leaders.
Following the incident, Mizanur Rahman Sumon of Chandpur’s Hajiganj filed a case against 62 named people, including Golam Parwar, with Motijheel Police Station.
The investigation officer of the case and Sub Inspector Awal Hossain submitted a charge sheet against 97 people to the court on September 30 of 2013. Of the accused, one Abdur Jobbar died during the case proceedings.