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| Position | Top player | Team ranking | Top prospect | Organizational ranking | Overall ranking |
|---|---|---|---|---|---|
| Catchers | Joe Powell | 13th | Juan Arrey | Tied for 17th | 16th |
| First Basemen | Jamie Gerdes | 6th | Bill Vargas | Tied for 17th | 9th |
| Second Basemen | Markus Deacon | 14th | Nelson Maldonado | 9th | 13th |
| Third Basemen | Pedro Zapata | 9th | Travis Harris | 5th | 8th |
| Shortstops | Roman Contreras | 11th | Manny Ruiz | 11th | 10th |
| Left Fielders | Joe Swanson | 14th | Dave Hargett | 3rd | 12th |
| Center Fielders | Juan Ybarra | 16th | Seung-woo Kim | 4th | 16th |
| Right Fielders | Josh Bradshaw | 15th | John Payne | 1st | 15th |
| Starting Pitchers | Éric Rossi | 16th | Jeff Beigel | 14th | 18th |
| Relievers | Philippe Bourbon | 13th | Ryan Cicinelli | 2nd | 10th |
| Closers | Jim Schlenker | 17th | Brooks Rumsey | 16th | 19th |
