The Halacha prohibits "Bitul Keli MeHechano"-neutralizing a vessel from functioning on Shabbat. That is, one may not perform an action that would render an otherwise permitted vessel to be Mukse. The classic example is placing a bowl underneath a hen to catch her egg. The egg is Mukse as "Nolad"-an item that came into being on Shabbat. Once the egg falls in the bowl, the bowl becomes Mukse as a "Basees"-a base for Mukse.
Another case would be placing a vessel underneath a lit candle to catch the oil that drips. That oil is Mukse because it was designated for lighting. This is prohibited because when the oil drips on the bowl, it neutralizes the bowl from any other use.
The Mishna Berura (Rav Yisrael Meir Kagan of Radin, 1839-1933) discusses an interesting case brought by the Magen Abraham (Rav Abraham Gombiner, Poland, 1637-1682) in which one neutralizes a vessel by "Gerama"-indirect means. For example, if there was a drip of oil from a hanging lamp on to the table. If one placed a vessel under the table, is it permitted to then move the table to expose the vessel and catch the drip? The Magen Abraham rules that it is permitted to do so, because he merely moved the obstacle and the bowl became aligned "automatically."
Similarly, the Gemara deals with a case of "Teruma Tehora" (pure gifts to the Kohen), which is not Mukse, and "Teruma Temeah" (impure gifts to the Kohen) which is Mukse, in the same basket. As long as both are in the basket, the basket may be moved. The Gemara permits removing the "Teruma Tehora" on Shabbat, leaving only the Mukse "Teruma Temeah," even though the basket becomes Mukse as a "Basees." This is permitted since, taking out the "good" neutralized the basket only indirectly by leaving the "bad" to remain.
This leniency can also be applied to a plate of food which also contains Mukse bones. It is permitted to eat all the food and leave only the bones, even though the plate becomes Mukse. Again, since the vessel was neutralized indirectly it is permitted. This is the conclusion of Hacham Yishak, as well.
One may rely on the lenient authorities and neutralize a vessel from use through indirect means.