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Shepley had practiced law in Bangor before moving to Portland and, as U.S. attorney for Maine, he knew numerous people throughout the state and elsewhere, and many of them corresponded with him or asked him for favors during the war.

Late in 1863 when Brig. Gen. Neal Dow of Portland and the 13th Maine Regiment was in a Confederate prison in Virginia, he and his son both wrote to Shepley, asking his help in getting Dow's clothing and other goods shipped from Louisiana to Maine.

Some historians who have written about occupied New Orleans saw Shepley as an extension of the disliked (and not particularly skillful general) Benjamin Butler. Some suggest Shepley was obstructionist toward Gen. Banks, Butler's replacement. When Shepley left New Orleans in March 1864 when a civilian government loyal to the Union was elected in Louisiana, he was assigned to the Department of Eastern Virginia, again serving under Butler and under Maj. Gen. Godfrey Weitzel, who also had been in the Department of the Gulf.

But Shepley – and all Union officers and politicians – were caught in a challenging situation. Louisiana had a number of Union loyalists, not all of whom shared the same views about what should happen to slaves, plantations, politics, or most other wartime and postwar issues. In addition, it was never easy to clearly distinguish a Union from a Confederate sympathizer, or to anticipate what their views and actions might be in an occupied city and state.

Shepley, like many other military officers also had to defend himself from various charges of misconduct or unfair treatment. Some were clearly political, such as that apparently made by Dr. Thomas Cottman, a supporter of secession, who tried to get early elections held in Louisiana. Neither Lincoln nor Shepley, who wanted to assure that any election would put those loyal to the Union in charge, would agree. Cottman managed to get "elected" early and was seated temporarily in Congress. He apparently blamed Shepley for his failure and made charges against him.

In addition, though, a number of New Orleans residents praised Shepley for his handling of the military government for two years and of his manner toward the residents and the issues they faced.

Shepley saved correspondence, copies of letters sent and received, and official documents from the 12th Maine Regiment and from his time in Louisiana, Virginia. Few personal letters accompany the official record.

Shepley's nearly four years in the army must have presented many personal challenges as well. He was 42 years old and had been widowed for two years when he enlisted. His three daughters were 15, 11, and 9 and apparently went to St. Louis for at least part of the war to live with Shepley's brother, John R. Shepley, and his wife, Mary, and their children. Shepley's father and mother, Anne Foster Shepley, lived in Portland and may have cared for the girls during part of the war.

When Shepley returned from military service, he resumed his law practice. He was soon offered a seat on the Supreme Judicial Court, but turned it down. He also had turned down the rank of brevet major general, preferring to keep his active duty rank of brigadier general.

Shepley's life resumed in Portland, but his personal challenges did not. In 1866, his mother died; in 1868, his youngest daughter died at age 16.

In 1869, Shepley was named judge for the newly established First U.S. Circuit Court.

During the presidential election campaign of 1864, Shepley was sought after in Maine and elsewhere as a speaker to talk about the state of the war and about Lincoln. Although he was a Democrat before the war, Shepley became a Republican afterwards and was a frequent speaker at Republican events during the 1868 elections. He had been elected to the Maine Legislature in 1866 as a Republican.

Shepley remarried in May 1872. He and Helen Merrill Shepley, who had been a nurse during the war, were married for six years, when, at age 59 George F. Shepley died "of a disease resembling Asiatic cholera."

Nathan Webb, U.S. District Attorney in Maine, said of Shepley, "His strength seems to grow with the drafts made on it." He called him "conspicuous and influential, distinguished for his eloquence and earnestness."

Shepley's law partner, A.A. Strout said, "His public spirit led him to take an active interest in every enterprise calculated to advance the prosperity of the city, and his generosity embraced every worthy object of public and private charity. He gave freely, but not for applause."

Nathan Clifford, a pro-slavery Democrat, who had served in the Maine House, the U.S. House, as U.S. Attorney General and who served on the U.S. Supreme Court from 1858 until his death in 1881, said of Shepley, "His duties were both civilian and military and in both he manifested great prudence, energy, and ability, which were repeatedly commended throughout the country."