A refinery was a facility that processed raw materials into more usable forms.
Bavali Station was a Federation deuterium refinery constructed inside Bannon's Nebula in 2259. (SNW: "Lost in Translation")
In 2369, Grand Nagus Zek congratulated Nava on completing his takeover of the arcybite mining refineries in the Clarius system. (DS9: "The Nagus")
In 2371, Lieutenant B'Elanna Torres proposed to convert USS Voyager's auxiliary impulse reactor into a crude dilithium refinery. (VOY: "Phage")
Also that year, Chief Miles O'Brien and Jake Sisko attempted to convert one of Deep Space 9's ore processors into a deuterium refinery, though in the process they inadvertently activated a counter-insurgency program left behind by the Cardassians. (DS9: "Civil Defense")
The Moneans operated extensive oxygen refineries in the Waters to extract oxygen from the water. In 2375, after the Voyager crew discovered that the refineries were increasing the density of the planetoid and threatening its survival, Lieutenant Tom Paris and Riga attempted to destroy the Moneans' primary oxygen refinery from the Delta Flyer. (VOY: "Thirty Days")
During the Dominion War in 2375, the Jem'Hadar destroyed a shipment of Tigan family pergium bound for the refinery on Rigel IV. (DS9: "Prodigal Daughter")
In 2377, Tebbis told The Doctor that he would be sent to work in a refinery with his father if he was cured of his chromovirus infection. (VOY: "Critical Care")