When the Civil War ended in 1865, Slough resigned his commission and opened a law office in Washington, D. C. In January 1866, United States President Andrew Johnson, appointed him to serve as chief justice of the New Mexico Territorial Court. One of his first and most personal acts was to seek funds to mark the graves of the Union dead and place monuments at the Civil War battle sites of Valverde, Apache Canyon, and Glorieta, New Mexico (only one in Santa Fe was erected). He also arrived to reform the legal system. Among the cases with the greatest impact was his decision that Pueblo Indians were U. S. citizens, could testify in his courts, especially in land disputes, and were equals in the eyes of the court, a decision eventually upheld by the U. S. Supreme Court. In February, 1867, he attacked the system of peonage in New Mexico, in anticipation of the Federal law against debt peonage—involuntary servitude—signed by President Johnson March 2, 1867. His entire career was that of a reformer, and what he found in New Mexico he thought was akin to the slavery he had fought in the Civil War to defeat.