Judge Kristin Ruth, attorney James Crouch, and the assistant, Elizabeth Michelle Daniel, were named in indictments handed down Tuesday.
Crouch faces two counts of obstruction of justice, one count of conspiracy, and one count of altering documents. Ruth is accused of willfully neglecting to discharge the duties of her office. Daniel faces conspiracy and obstruction of justice charges.
The charge Ruth faces is a misdemeanor, while the rest are felonies.
Ruth resigned last month amid an SBI probe into how the cases were handled.
As ABC11 first reported in February, the senior resident Superior Court judge in Wake County - Judge Donald Stephens - asked the SBI to look into the matter after he was alerted to the issue in a letter from Wake County District Attorney Colon Willoughby.
In his letter, Willoughby said he found "a disturbing pattern of what may be unauthorized and illegal judgments."
The DA said in at least 12 cases, a person was convicted of DWI in District Court and then the case was appealed to Superior Court. After a period of time, the appeals were withdrawn, and the cases were sent back to District Court for resentencing.
In all 12 cases, Willoughby said Judge Ruth - who was not involved in either the original sentencing or the resentencing - entered what appear to be orders that change the effective date of the sentencing without notifying prosecutors.
Willoughby said the orders effectively backdate the convictions and would shorten or eliminate the mandatory suspensions of the defendant's driver's licenses.
"In at least three of these cases, it appears that Judge Ruth has issued limited driving privileges for defendant without legal authority to do so," Willoughby wrote.
In a statement Ruth said she signed numerous orders for attorney James Crouch "that should not have been signed."
"I must admit that, because I trusted Mr. Crouch, I did not read the orders when they were presented to me," she said.
"I believe my resignation is necessary to maintain the integrity of the judicial system," she continued.
While Willoughby's letter mentioned at least 12 cases, the indictments handed down Tuesday listed more than three dozen.
Ruth was first elected to the bench in 1998.