You need a ship equipped with a tractor beam. You need it to be present at the same location as the target civilian ship, probably at your capital or another populous planet.
You can then open the "individual unit detail" screen and select your tractor equipped ship (or double-click on your tractor ship in the task group screen), open the misc tab, and manually create a tractor link with any ship at the same location. The newly-tractored civilian ship then switches to your entire control in the tractor ship task group.
You're free to transfer it to a new task group, move it around, scrap it in a shipyard to recuperate ressources and components and fuel, or just delete or destroy it where it stands.