Free Flight mode in 3D works with any single unit in the fleet, except units with the "Spy" ability.
You can send a unit that is in high orbit with a "defence" order to free flight. Send a unit with "defense" to a high orbit and after reaching the orbit navigate to the fleet overview via the Fleet panel, select the unit and press the "free flight" button on the control panel.
When in free flight, the unit can move at local coordinates in a given direction, which can be used to search for hidden objects and fleets.
Sending or returning a unit out of high orbit stops free flight.