There are three conditions that must be met for one to be allowed to separate on Shabbat: 1) He must separate the Ochel (desirable food) from the Pesolet (undesirable substance), and not the other way around; 2) this must be done by hand, and not with a utensil; 3) this must be done just before the food is to be eaten, and not for later use. The reason why Borer is permitted for immediate use is because it is then considered part of the process of eating. Just as chewing is obviously allowed on Shabbat, and does not violate the prohibition of Tohen (grinding), similarly, separating the desirable food from the undesirable substance is permitted as part of the process of eating. It is therefore allowed immediately before eating, but not earlier.
How soon before the meal must this be done? When do we consider the Borer (separation) as taking place "immediately" before the meal such that it is permissible?
This issue is subject to debate among the Halachic authorities. The Bet Yosef (commentary to the Tur by Maran Rav Yosef Karo, author of the Shulhan Aruch), in Siman 319, cites the Mordechi (Rav Mordechai Ben Hillel, Germany, 1250-1398) as saying that as long as the separating is done within an hour of the meal, this suffices to allow Borer. The Ben Ish Hai (Rav Yosef Haim of Baghdad, 1833-1909), in Parashat Beshalah (1), takes this ruling literally, and permits separating food up to an hour before the food is to be served.
Others, however, explained the Mordechi differently, claiming that he did not actually refer to a full hour before the meal. The Shebet Halevi (Rav Shemuel Wosner, contemporary) claimed that the Mordechi meant a half-hour before the meal, and thus one may separate only until a half-hour before the food is going to be served. Others rule even more stringently. Rabbi Moshe Halevi (Israel, 1961-2001), in his work Menuhat Ahaba (vol. 2), notes that from the beginning of the Mordechis comments, it appears that he requires the separating to be done immediately before the food is served. This is the ruling accepted by Hacham Ovadia Yosef, in Hazon Ovadia (p. 180, Halacha 5; listen to audio recording for precise citation), where he writes that Borer is allowed only if it is done within a few minutes of the meal. Hacham Ovadia notes that this was the position of the Hazon Ish (Rav Avraham Yeshaya Karelitz, 1878-1953), who ruled that separating may be done no earlier than five minutes before the meal. He adds that in a situation where one is preparing a very large meal for a large number of people, and many foods need to be prepared, then one may begin the preparations already a half-hour before the meal is scheduled to be served. In an ordinary case, however, when a woman is preparing a meal for her family and simply needs to peel some fruits or vegetables, and perhaps separate the leaves of lettuce from the spoiled leaves, this should be done only within a few minutes of the meal, and no earlier.
This means that a woman should not do separating in preparation for Shabbat lunch before she goes to the synagogue on Shabbat morning. Of course, other preparations are permitted early in the morning, but preparations involving Borer may not be done earlier than a few minutes prior to the meal, or within a half-hour if many guests will be attending, as discussed.
Summary: One is allowed to separate desirable food from an undesirable substance on Shabbat if this is done by hand and within a few minutes of the meal when it will be served. If one needs to prepare for a large meal with many guests, then the separating may be done within a half-hour of the meal, but no earlier.
