The fundamental concepts and process are simple, but getting good results is difficult unfortunately. Basically all you need to do is put your camera straight above the terrain you're exporting, aim it down at the ground -90 degrees, and do a square render. Orthographic camera would work best, or you can get your camera really far away then zoom in to the area you want to capture. This will reduce distortion.
To get best results you'll want to turn off the atmosphere, and use lighting that is as neutral as possible. Then render at as high a resolution as you can, start with something like 2000x2000 pixels. You'll probably need a good deal more than that but your system's RAM may not support it. Worth trying though. You could also try rendering in separate crops. For this kind of render you won't need GI or much antialiasing either so I'd turn GI off and AA down to something like 3.
That should get you a start, at least to see if it's even workable for your needs.
- Oshyan