A nude model
A nude Q
Nudity refers to not having any clothes on. Most species must be naked to have sexual relations. Humans and Vulcans considered nudity to be somewhat risqué and titillating. The Edo considered nudity a normal part of everyday life, however. (TNG: "Justice")
In 2266 On Planet Exo III Captain James T. Kirk was stripped nude and placed on an android duplicator in order for Dr. Roger Korby, the long lost fiance' of Christine Chapel, to create an android duplicate of Kirk to take over the Enterprise in order for Korby to populate the universe with other androids. (TOS: "What Are Little Girls Made Of?")
Betazoid wedding ceremonies are traditionally held in complete nudity, including the participants and the guests. ("Haven", et al.)
When Q was stripped off his powers by the Q Continuum he appeared nude on the bridge of the USS Enterprise-D. (TNG: "Deja Q")
Tuvok slept in the nude and dreamed of forgetting to put on his uniform before reporting for duty. (VOY: "Waking Moments")
A line in Henry V stated, "For though I speak it to you, I think the king is but a man, as I am. The violet smells to him as it doth to me, in his nakedness he appears but a man." (TNG: "The Defector")
In 2369 Captain Jean-Luc Picard was stripped off his clothes by the Cardassian Gul Madred as part of his torture and interrogation. (TNG: "Chain of Command, Part II")
Appendices
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Background information
Gene Roddenberry originally intended for his vision of Earth to be a civilization of nudists. (Star Trek is...)
According to the Star Trek: The Next Generation Companion, for the episode "Unnatural Selection", "the Darwin "superchildren" were originally to have appeared nude and the extras were asked to shave from the neck down. But the use of transparent furniture quickly nixed that idea, and costumes were hastily made as the extras endured stubble itch."