In the original ending, the WTC towers opened up, releasing a swarm of UFOs. Following 9/11, the ending was changed. However, you can still see a sign for the WTC exit on the freeway.

Originally set for release in 2001, this Al Pacino movie was delayed until early 2003. It contained several shots of the WTC towers that were removed.

Rock Star was released a week before 9/11. While it didn't contain any shots of the WTC towers, the towers did appear briefly in the trailer for this movie.

Serendipity was released less than a month after 9/11. All shots of the WTC towers were edited out of it.

You have to look fast to see the brief glimpses of the WTC towers that the producers chose to leave in the background. However, they did remove the towers from the poster and trailer.

Originally set for a December 2001 release, it was moved to March 2002 while producers decided to remove a scene where pieces of a destroyed Moon destroy buildings in New York. The movie never contained shots of the WTC towers, but producers didn't want to bring up memories of the terrorist attacks of 9/11.

Zoolander was released just weeks after 9/11. One shot of the WTC towers was removed from the movie, and one shot was altered to obscure them. (I believe this is one of the altered shots.)

New York skyline scenes were edited to remove the WTC towers before it was released in 2002.