Strictly speaking reconstruction of the South following the Civil War does not meet the textbook definition of colonization: colonies are a source of raw materials and a market for manufactured goods. However, in one adopts a more liberal definition, namely the complete domination of one portion of the country by the other without the consent of the dominated portion, then reconstruction is a classic example of internal colonization.
Congress was dominated by Radical Republicans following the end of the war, the most extreme of whom were Charles Sumner of Massachusetts and Thaddeus Stevens of Pennsylvania. Sumner's position was that the former Confederate states had "committed political suicide." Stevens argued that they had become little more than "conquered provinces." They were determined to see that the South became a mirror image of the North, and insisted that Congress had the authority to do so by reason of its mandate in the Constitution to guarantee to each state "a republican form of government."
The former Confederate states did not help their own position by being bitter and recalcitrant in defeat: Alexander Stevens, former Vice Presidency of the Confederacy, was elected to the Senate in the election of 1866. Needless to say, the Senate refused to seat him. Ultimately, Congress established a Joint Committee on Reconstruction and also passed the Military Reconstruction Act which placed the South under military rule; fifteen districts with a military governor. The military governor controlled who could sit on state conventions to draft new constitutions.
With the South subject to military control and under the absolute control of Congress, the argument can be made that the South was an internal colonial dependency of the North.