Expanding upon what mezzoprezzo (Casper) has said, try using a digital elevation map (DEM) of an area you are interested in and build a route on it. You can take an area that never had a rail line and survey your own route. Put in the forests, houses and roads as they're laid out on the map, but put your tracks in where you want. This can become an interesting route as you plan bridges over waterways, roads, and valleys, as well as plan for stations and road crossings. I did this for a portion of my route, and by far this the most interesting and most fun section to drive.
Another alternative to generating the terrain by hand is to use a displacement map. This is a gray scale image that converts light and dark into height information. This can produce an interesting landscape that will also present a challenge when it comes to placing tracks and building the ROW for your route.
John