I am assuming dirt/fill, for the east-west passages. based on the following from Google:
Grand Central North
Grand Central North, opened on August 18, 1999, provides access to Grand Central from 47th and 48th streets. It is connected to the Main Concourse through two long hallways, the Northwest Passage (1000 feet long) and Northeast Passage (1200 feet long), which run parallel to the tracks. Entrances are at the northeast corner of East 47th Street and Madison Avenue (Northwest Passage), northeast corner of East 48th Street and Park Avenue (Northeast Passage) and on the east and west sides of 230 Park Avenue (Helmsley Building). Ellen Driscoll, an artist from Brooklyn, designed the mosaics in Grand Central North.
The entrances to Grand Central North were originally open from 6:30 AM to 9:30 PM Monday through Friday and 9 AM to 9:30 PM on Saturday and Sunday. As of summer 2006, Grand Central North was closed on weekends, with the MTA citing low usage and the need to save money by the shutdown [2]. Prior to the closing, about 6,000 people used Grand Central North on a typical weekend [3], and about 30,000 on weekdays.
Ideas for a northern entrance to Grand Central were floated around since at least the 1970s. Construction on Grand Central North lasted from 1994 to 1999 and cost $112 million. It was originally scheduled to be completed within three years on a budget of $70 million. Delays were attributed to the incomplete nature of the original blueprints of Grand Central and previously undiscovered groundwater underneath East 45th Street. As of 2006, the passages are not air-conditioned.
The depths of the passages in relation to the terminal are:
Metro-North Railroad upper level, 20 feet below street
Northwest and Northeast passages, 20 feet
47th Street cross-passage, 30 feet
45th Street cross-passage, 50 feet
Metro-North Railroad lower level, 60 feet
If I remember the West passage is over the former Track 31, which had a platform, but it did come all the way in as far as the other tracks. For the East Passage, I do not remember what was replaced.