We present how basic logic gates including NAND, NOR and XOR gates can be implemented counterfactually. The two inputs (Bob and Charlie) and the output (Alice) of the proposed counterfactual logic gate are not within the same station but rather separated in three different locations. We show that there is no need to pre-arrange entanglement for the gate, and more importantly, there is no real physical particles traveling among Alice, Bob and Charlie during the information processing. Bob and Charlie only need to independently control the blocking and unblocking of the transmission channels that connect them to Alice. In this way, they can completely determine the state of a real photon at Alice's end, thereby leading to implement a counterfactual logic gate. The functionality of a particular counterfactual logic gate is determined only by an appropriate design of Alice's optical device. Furthermore, by utilizing the proposed counterfactual logic gates, we demonstrate how to counterfactually prepare the Greenberger-Horne-Zeilinger state and W state with three remote quantum objects, which are in superposition states of blocking and unblocking the transmission channel.