Hi,
The 3D modeling program used to create the tunnel would normally also be used to make the part to fill in the land around the opening, but, that normally only works well if the tunnel is built for a particular project/model/map. All the other uses would be for a more generic use, and then normally a larger tunnel portal is built, like the built in fixed to a grid point tunnel in Trainz.
If using a tunnel made by someone else, often they would - I presume - have also modeled portals to go with it, either as various grass type of splines or other ways to put around the opening.
All would have to be modeled in a 3D creating program, as in Trainz, the smallest hole one can make is a huge 10m square, and it can be very hard to know how big a portal area one needs to make unless one has a specific area in mind when creating the tunnel in the first place.
Hope this helps some?
Linda