If, however, one does not fulfill all three of the above conditions, even if he has fulfilled the one or two of them, he has violated the melachah (see Shulchan Aruch 319:1). For instance, if one separates items using a utensil that is designed to separate (e.g. a sieve, funnel, strainer, colander), even though he removed the good from the bad with the intent of immediate use, since he was lacking in the third condition, he has violated the melachah. This begs an obvious question: if one may only use his hand to separate, how can one ever use a kli [e.g. a knife or a fork] to separate?

The Poskim (Shu"T Igros Moshe OC 1:124, Shu"T Minchas Yitzchok 1:71) explain the prohibition is only if one uses a kli that assists and creates a more effective sorting; however, if he could have sorted just as well without the utensil, then the utensil is considered merely as an extension of his hand and permitted. He is just using a kli either because he does not want to get his hands dirty or it is too far to reach with his hands.
Accordingly, there is no blanket rule which specific utensil is always permitted or always prohibited, rather it all depends on whether you could have sorted just as well with your hand or not. For example, the Shulchan Aruch (319:14) rules it is permitted to pour wine away from the dregs in the bottle of the bottle and the Mishneh Berurah [319:55] explains the Shulchan Aruch is only talking about a scenario where one plans on not using the wine immediately, for if he intends to use it immediately, he would be sorting "the normal way of eating", which is permitted. It is clear that even though he is using a kli (the pitcher) to separate, since he technically could have separated the wine just as well, the pitcher is considered "an extension" of his hand.

Consequently, one may use a fork to select the food he wants from a mixture, since in this case the utensil being used is no more instrumental in the selection than he could have done with his own hand. Similarly, a person can use a spoon to remove solids from liquids [e.g. vegetables from soup], since the spoon is not doing a better job of sorting. If, however, there is only a small amount of noodles, etc. remaining in the soup, since such a small quantity cannot be easily removed with one's hands, to use a spoon or fork to remove them would be assisting a person to separate in a better fashion and would thus be prohibited (Shu"T Igros Moshe OC 1:124).

On a similar note, one may use a knife to peel fruits or vegetables even if the knife is separating in a more efficient way than one could do with his hands, since it is absolutely natural to peel fruit with a knife during the meal, so this is considered derech achilah (Zachor V'Shamor pg. 288).

Additionally, one may use the rim of a pot to strain soup from undesired noodles or vegetables, by tilting the pot so that the soup slowly runs over, since as a straining device the rim of the pot will not strain better then one's hand (Shu"T Igros Moshe OC 1:124). However, according to most Poskim, using a pot cover by pouring soup from a pot using both the pot and the lid is similar to a strainer and therefore prohibited (Harav Moshe Feinstein, zt"l [Shu"T Igros Moshe OC 1:74:1, Shmiras Shabbos K'Hilchisa).