Trimming 3D Mesh Without adding extra vertices

Hi, 

I am creating a 3D model for a proposed Highway and I need to trim the limits of the mesh for breaks in the road at bridges. I have found a couple different ways to trim the mash to match the correct limits, however, each method creates a bunch of extra vertices. The top surface i still drawn in correctly which is good, however for turning in final plans I would like to have a more aesthetically pleasing model. 

Below is a summary of each method I have used to clip the mesh. There appears to be no rhyme or reason to why the extra vertices pop in, because one side will do it and another will not and it varies, sometimes it will add them and other times it will not.

Please let me know if anyone first of all knows why it is doing this, how to trim the mesh object without adding the extra vertices and if someone has a better or more efficient way of trimming the mesh objects I am open to suggestions.

Thanks, 

Layton

The first method I used to trim the model is using a fence clip to trim the mesh back to the limits. The pictures below show the begining and end result of the trimming. As you can see in the second picture there are extra vertices drawn in the components fence. 

The other method I tried using was the "Mesh Project" Tool: 

I had similar results using this tool as shown by the pictures below.