The last of the carriages has been lifted from the site of the fatal train derailment near Stonehaven.
Driver Brett McCullough, conductor Donald Dinnie and passenger Christopher Stuchbury died in the crash on Wednesday, August 12.
The Aberdeen to Glasgow commuter service came off the tracks after striking “a pile of washed-out rock and gravel”, a Network Rail interim report said.
The process of recovering the vehicle, using a 600-tonne crawler crane, began two weeks ago. The last of the carriages left the site on Friday.
Damage to the track and bridge has been described as “quite significant”, with the repairs needed to be outlined in the coming days.
A Network Rail spokesman said: “We’re now beginning the process of assessing the repairs required at track level and on the embankments.
“There’s quite significant damage to the track and bridge involved in the incident.
“We expect to be in a position to confirm works required and timescales over the next few of days.”