Daniel J. Wineski is charged with second-degree sexual assault of a child, intimidation of a victim, false imprisonment, and three counts of misconduct in office.
The court entered a not guilty plea on his behalf.
Authorities say in 1996, Wineski forced sexual contact with a 14-year-old girl and threatened her with a gun to keep the incident from being reported.
La Crosse County Judge Ramona Gonzalez presided over the hearing after a Trempealeau County judge refused himself because of familiarity to Wineski.
Today, the defense requested a substitution, which would appoint a third judge to the case.
If convicted, Wineski faces 33 years in prison