As mentioned in comments, this is almost certainly Space: Above and Beyond.
- Based in space on an alien planet
The main characters were based on a "space carrier" the USS Saratoga, but many episodes were set on alien planets
- there is conflict with any alien race
The Chigs
- the main character is a pilot? Marine?
The main characters were members of the 58th Squadron Space Aviator Cavalry, United States Marine Corps
- the big thing I remember is the main characters sister is missing, she landed on the planet before him. Finding her is the long running story arc
Lt. Nathan West had a fiance who travelled to a colony world that was then attacked by the aliens before he arrived.
- late nineties aired on a major network
First screened on the FOX network in the USA between 1994 and 1996
- the whole series felt like it was filmed at night
There were a lot of scenes in space and a some on alien worlds at night