To allow ID Tech 3 games (including Quake 3, Star Trek Voyager: Elite Force, Return to Castle Wolfenstein and many more) to run using a widescreen or custom resolution you can edit the configuration file created after you first run the game.
In the case of Star Trek Voyager: Elite Force, that configuration file is located in
The first change you need to make, is you need to find a configuration line that says the following;
seta r_mode "x"
Then, either change or add the following two lines;
seta r_customwidth "x"
seta r_customheight "y"
y are the width x height values for the resolution you wish to run, in this instance 1920x1080.
Finally if you want to adjust the field of view drawn in game, you can do so by changing or adding the following;
seta cg_fov "x"
x is the field of view in degrees, defaulting to 90.
The ID Tech 3 engine does not natively support "Fullscreen Windowed Mode", and thus neither does Star Trek Voyager: Elite Force. However there is this nice article on Steam which details how to make any game run in fullscreen windowed mode, and I have tested this with Elite Force and it works fine.