Many of the changes to the design have to do with the space below ground, where trucks bringing goods to the offices and stores in the new buildings will pass through security screening. Victims' family members have long been calling for the "footprints" where the Twin Towers stood (marked in squares on the map) to be free from any construction besides a memorial, both above and below ground. While the original plans put the security checkpoint underneath the World Trade Center site, the new design moves the underground truck route south of Liberty Street, underneath the new park. The truck ramp and security area is marked in blue in the image on the left.

The PATH tracks, which ran underneath part of the north tower and much of the south tower before the attacks, are being rebuilt in the same location, although an extra train platform may be added. The PATH tracks are shown in the image on the right. The PATH station is slated to open in November 2003.