I use the bspconv tool (http://nate.scuzzy.net) to convert Quake3 bsp files to a simpler format and then use them in my 3d engine. When you build maps in Q3Radiant you build walls, floors, everything as boxes not as polygons. Why? Has it something to do with bsp trees (which I don''t know anything about) ? This is a big drawback for me because I have to draw 24 polygons instead of 6 for a simple room(box). Is there any better converting programs around that will remove these "unnecesary" polygons or any other "solution" for my problem?

It wouldn''t surprise me if the Q3 tools automatically did some sort of visibilty testing. I am not sure on that though.

I''m assuming that Quake3 is similar to the older quake engines in regards to the techniques used to determine visibility and bsp construction.
First imaginge that all 6 faces of each brush ("box") are made of 2 triangles, so each brush has 12 polygons (triangles).
The csg tool takes these triangles and looks for any intersections, splitting each poly along those intersections, so after it''s done, there won''t be any intersections left. Next is the bsp tool, which uses the polygon''s planes to divide the map and discard back-facing polys. This ends up with a map of just polygons, but I think that the map editors use brushes because manually placing polygons would be tedious at best.
In the quake engines, bsp is not used for visibility determination, it''s used for collision detection. Quake used a system called PVS (Potentially Visible Sets) which were basically a list of nodes possibly visible from the current position.
Anyway, I hope my alcohol assisted explanation helped more than it hurt.
To better understand the process, download and experiment with the actual map tools sources, it''s educational if nothing else

Feel free to email me.