In some cases the initial topography is so poor that the images won't align. If you are tiling the script will throw out all images, then delete the landmark since there are no images. Other times there just are not enough common features in the images for you to determine how to manually align the images. Here is how to fix that problem.
If the landmark was deleted, you'll need to grab the initial part of the INN file and paste that into LITHOS. You'll want to paste in everything before the first auto-align (i.e. 1-0-1). If the landmark wasn't deleted than you can just load the landmark like normal.
The basic steps will be as follows:
1. Zoom out enough that you can see features to which you can align. You'll want to load base topography from somewhere so you have a start place. 2. Align features by hand, then build topography until the images can auto-align. Save the landmark. 3. Zoom in to the original resolution, then load the topography from the landmark you just saved. Yes: this means you'll be loading base topography from a landmark into itself. 4. Now the topography should be good enough that you can resume fixing the landmark.
Normally the above steps are unnecessary because you can just load base topography from a bigmap. However, on several occasions the topography from the bigmap just won't work. By building topography at a low resolution, zooming in, then loading the topography you just created, it ensures the images you are working with will align.
Another solution, will is faster but may not always work, is (instead of zooming out), just load the base topography from a lower resolution landmark. However, since the bigmap you created was derived from these lower resolution landmarks and failing, chances are the lower resolution landmarks will still fail.