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| Position | Top player | Team ranking | Top prospect | Organizational ranking | Overall ranking |
|---|---|---|---|---|---|
| Catchers | Ronny Paulino | 21st | Dusty Brown | 19th | 21st |
| First Basemen | Brad Wilkerson | 21st | Sandy Madera | Tied for 10th | 12th |
| Second Basemen | Marcus Giles | 6th | Joe Thurston | 3rd | 2nd |
| Third Basemen | Troy Glaus | 17th | Martin Prado | 1st | 9th |
| Shortstops | Abraham Nunez | 21st | Mike Aviles | 3rd | 7th |
| Left Fielders | Barry Bonds | 3rd | Tied for 19th | 13th | |
| Center Fielders | Nate McLouth | 20th | Tied for 23rd | 26th | |
| Right Fielders | Alfonso Soriano | 15th | Hunter Pence | 6th | 6th |
| Starting Pitchers | Rich Harden | 14th | David Pauley | Tied for 17th | 19th |
| Relievers | Mike Jackson | 22nd | Jeremy Accardo | 25th | 25th |
| Closers | Robb Nen | 19th | Chris Ray | 25th | Tied for 27th |
