I think FEFLOW could not directly handle contout lines. I do that mostly in the following way:
- create in ArcView or ArcGis a Surface TIN from the contourlines
- export the FEFLOW nodes as points (shapefile) and load them in the GIS
- extract the elevation from the surface TIN at the points and add them to the shapefile
- import this to FEFLOW
This is a little bit amfward, but it works.