I Recently downloaded some FS98 scenery, i put it in cfs2. every thing works great, but the runways. You see the runway "floats" about 300 ft above the ground.
Is there a way to fix this?

CFS2_Person

One thing to try though is while in the game settings, set the scenery display up to max. Some scenery is created to properly display at a high setting only.

When you start your game, go to "Settings". At the top of that screen you see "Overal Image Quality". Select "5" or "6" and then check your floating runway out. If it is still floating, then it is a problem with the FS98 scenery displaying properly in CFS2.
Then you can only remove it as you won't be able to fix this. Sorry. FS2000 is more compatible with CFS2 than 98 stuff. I would recommend that you stay away from that.

Your problem sounds like a "Flattening" issue. 

CFS2 has an explanation in the installed documentation (see "Readme" doc in CFS2 main directory, pages 7 & 8). 

Due to how CFS2 handles terrains and elevations, the Flattening option basically takes your add-on scenery (i.e. FS98) and sets it to a certain elevation by specifying it as a four-point rectangle and the elevation.  The flatten switch is inserted into the [Area xxx] description block of your Scenery.cfg file.  It took me a couple of re-reads to understand the instructions. 

You will probably have to play with a number of settings for the elevation and it may not perfect.  You may find some of your terrains phasing in and out based on your point of flight.  Use your "Shift-Z" option to get the Long/ Lat coordinates while in the add-on scenery and insert those into the Flatten switch.

Hope this solves your problem.

MH