Shells and peels of food which are edible, even if only to animals, are not Mukse. For example, the Shemirat Shabbat K'hilhata (Yehoshua Yeshaya Neuvirth, Jerusalem 1927-1913, Ch. 20:27) rules that orange peels, watermelon pits and soft bones are not Mukse and may be handled on Shabbat. He goes as far as to say that even if these items were already put in the garbage, they are not Mukse.
On the other hand, there are foods which are Mukse on Shabbat. For example, flour or raw rice are Mukse because they are inedible and may not be prepared on Shabbat. Regarding raw potatoes, the Shemirat Shabbat K'hilhata is stringent, although the Menuhat Ahaba (Rabbi Moshe Halevy, Israel, 1961-2001) was lenient, since they are edible under extenuating circumstances. Similarly, all types of raw meat are not Mukse, since it can be consumed. Therefore, if a woman left raw meat on the counter before Shabbat, she may place it in the freezer on Shabbat. Frozen raw meat in the freezer may be moved, as long as it could be thawed out before the end of Shabbat.
Food which is Asur B'hana'ah-forbidden to benefit from, such as Hames on Pesach, is Mukse. Therefore, it is prohibited to handle or rearrange Hames items on Shabbat and Yom Tob of Pesah that have been sold to the non-Jew before Pesah. Similarly, fruit which is Orlah (within the first three years) or food upon which a vow of forbidding benefit has been taken, are also Mukse.
Watermelon pits, orange peels, soft bones, raw potatoes and raw meat are NOT Mukse.
Raw rice and flour ARE Mukse, as well as food items that are forbidden to benefit from, such as Hames, Orlah and foods upon which there is a vow forbidding benefit.