In legal circles, McQuillan was most noted for his work and expertise in the complete revision of the New York State penal code in the 1960s, the first major overhaul of that law since the 1800s.
He also co-wrote an independent review of flaws in the criminal case mounted against Jeffrey Deskovic, an upstate New York man who spent half his life in prison for a rape and murder he did not commit.
After McQuillan left to become director of the State Office of Crime Control, there were additional revisions to the code and the final draft took effect as law on September 1, 1971.
In 1985, McQuillan was also named administrative judge of the criminal branch of the State Supreme Court, a position he held until his retirement.
McQuillan based his ruling on a 1986 New York State Court of Appeals decision calling for a reversal of a conviction whenever the prosecution withholds evidence.
An attempt to appeal this ruling was rejected by the Appellate Division of the New York Supreme Court, and in 1995, the Manhattan district attorney's office said it would not retry Wahad.
The review was commissioned by the newly elected Westchester County district attorney Janet DiFiore and was written by McQuillan along with Leslie Crocker Snyder, William L. Murphy; and Richard Joselson.
In a 1972 legal ruling, he urged the state legislature and governor to change laws that provided for automatic exemptions for women from jury duty.
He also was a member of the Criminal Jury Instructions Committee and served on a task force formed by NY Governor Hugh Carey to study ways to increase state funding for local police departments.
In 1993, he received the New York State Bar Association's Vincent E. Doyle Jr. Award for Outstanding Judicial Contribution in the Criminal Justice System.