School officials said a contractor cut back the trees based on advice from a committee that's been trying to save the oaks since their poisoning was discovered in early 2011.
The work was done between summer and fall semesters while there were fewer pedestrians and cars on campus.
A University of Alabama fan is awaiting trial on charges of spiking the trees with a powerful herbicide after Auburn beat the Crimson Tide in 2010 on its way to the national championship, and a Lee County judge has barred anyone involved with the trees and the case from public comment.
Leaves on the trees are mottled and brown, and the canopies aren't as large as they once were. But in a written statement, school officials indicated the trees were in good enough shape for Auburn fans to plan on gathering this fall after victories.
"While long-term decisions about the trees have not been made, fans are still welcome to gather at the corner this fall and continue the tradition of rolling the trees with toilet paper," said the brief statement.
Harvey Updyke, an avid Alabama fan, is charged with poisoning the trees. His trial, which originally was set to begin in June, was delayed until Oct. 1 after Auburn's student newspaper published a story reporting that Updyke confessed to a reporter outside the courtroom.
Updyke, who named a daughter Crimson Tyde and a son named after legendary Alabama coach Bear Bryant, has pleaded not guilty by reason of mental disease or defect to charges that include criminal mischief and desecrating a venerable object.
Defense attorneys have asked a judge to move the trial, citing extensive publicity in the Auburn area. If held as currently scheduled, the trial would fall between Auburn home games against Southeastern Conference rivals LSU and Arkansas.
(Copyright 2012 by The Associated Press. All Rights Reserved.)