http://www.baseballamerica.com/minors/ask-ba-2/
Ask BA: How Do The Minor League Phases Of The Rule 5 Draft Work?
Teams can choose to shield eligible players from selection in the major league phase of the Rule 5 draft by adding them to the 40-man roster. (The deadline to make 40-man additions usually falls on or around Nov. 20.) The player pool of Rule 5 eligibles consists of two main groups:
• Those players who signed at age 18 or younger five years ago, such that the majority of players signed out of high school or internationally in 2009 become Rule 5 eligible for the first time this year.
• Those players who signed at age 19 or older four years ago, such that the majority of players signed out of college or junior college in 2010 become Rule 5 eligible for the first time this year.
In the Triple-A phase of the Rule 5 draft, teams may select any eligible player left off the major league 40-man roster or the Triple-A reserve roster of 38 players. In the Double-A phase of the draft, teams may select any eligible player left off the major league roster, the Triple-A reserve roster or the Double-A reserve roster of 37 players. In other words, a player selected in the Triple-A phase does not rank among his organization’s top 78 talents, and a Double-A selection does not rank among its top 115. In these cases, players are not required to remain on a particular roster. The player’s contract is irrevocably assigned to the drafting team and the drafting fee ($12,000 for Triple-A, $4,000 for Double-A) is paid.
June 5 is used as the cutoff point at which a player’s age is determined, and players who sign after the minor league season concludes—typically on Labor Day weekend—don’t have their Rule 5 clocks begin ticking until the following season. Any eligible player can be selected for the Rule 5 fee of $50,000 (payable to the original team) and then must be kept on a major league roster for the following season. If the player doesn’t stick, then he’s placed on waivers and—if he clears—is offered back to his original team for $25,000.