Commander Cliff appears as a playable multiplayer character in The Second Encounter only, but not in Serious Sam HD: The Second Encounter. He is, however, fully playable in the Xbox LIVE Arcade version of Serious Sam 3: BFE multiplayer, despite being cut from the PC version of the game.
Commander Cliff, using the Serious Sam HDZorg Commander model, can be found in the Serious Sam 3: BFE game files. It seems that Commander Cliff was supposed to be playable at one point, but was cut for unknown reasons. However, with some file editing, he is fully playable.