(written from a Production point of view)
Chroma key, also known as blue screen or green screen, was a colored backdrop used for shooting scenes whose backgrounds would later be filled in with CGI scenery.
One typical application of the technique was using it to film footage that would be inserted into the main viewscreen in the Star Trek: Deep Space Nine Ops set. "Although we do call it a blue screen, it's actually green because we're using blue neon surrounding the screen," explained Production Designer Herman Zimmerman. "We use a green saturated color, but you can key off of any saturated color." (Captains' Logs Supplemental - The Unauthorized Guide to the New Trek Voyages, p. 16)
The call sheet for the episode "The Andorian Incident" listed a green screen in the mess hall scenes, replaced later in post-production by a moving starfield. Another green screen was used during filming of this episode and raised on a platform for a view through a metallic door in a Vulcan reliquary, depicting later a CGI-created matte painting of a Vulcan listening post. ("The Andorian Incident" call sheet)
A green screen was also used and placed on the monitor in Archer's quarters at the beginning of the first season episode "Fortunate Son". Later, the monitor was "filled" with a recorded message from Admiral Maxwell Forrest. ("Fortunate Son" call sheet)