Alien refers to any being that is foreign to one's own homeworld. The term can be used affectionately or as xenophobic slang.
Prior to their identification, the Takret were called alien by T'Pol. (ENT: "The Catwalk")
The 22nd century inhabitants of Earth referred to the Borg as aliens, as the species was unknown at the time. (ENT: "Regeneration")
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Background information Edit
According to the TNG Season 1 Writer'/Directors' Guide, the term "alien" was defined as "not Human. Different. Not of our tribe. An alien being is any life form not native to Earth."
Behind the scenes of Star Trek Into Darkness, the alternative term "visitor" was used for non-Humans.