You're welcome. Glad to heat, that it helped. I'm afraid at the moment RailClone doesn't include any "capping holes" feature. A Cap Holes feature was available in the first betas of RC 2.4, but we had to remove it, because of an unsolvable problem with the mapping coordinates. It's still on our wish list, but very difficult to solve due to problems with UVWs and the way in which some slices occur.
You can apply the Cap Holes
modifier to the object though this has the same limitations as we encountered in RC 2.4 and also this will disable instancing.
Let me add, that if you are using V-Ray, you might find handy the VRayDistanceTex
map to perform a render-time boolean (and optionally also a capping effect) as explained in this post