In 1989, he was indicted for racketeering and obstruction of justice. Specifically, it was alleged that Aguilar, at the request of Abe Chapman (a convicted narcotics trafficker), tried to influence another judge, Judge Stanley A. Weigel, on behalf of Michael Rudy Tham, a former Teamsters official who was appealing an embezzlement case against him.[3] On March 19, 1990, the case ended in acquittal on Obstruction, and in a mistrial on the other counts.[4] He was retried over the summer and convicted on five counts.[5] and sentenced to six months in prison, 1,000 hours of community service and fined $2,000 on conviction of unlawfully disclosing a Government wiretap and obstructing justice by lying to Federal agents about it. He continued to be out on bail while his appeals took place and refused to resign. In 1993, he faced impeachment proceedings, but they were put on hold when the conviction was overturned the following year.[6] For this reason, he was able to assume senior status on April 15, 1996, but chose to retire two months later on June 24, 1996.
Post judicial service
Aguilar returned to the private practice of law in Santa Clara County, from the time of his retirement from the federal bench until 2015, when he retired from the bar.[7] He died on December 2, 2020, aged 89.[2]