You can set a border for a site model easily in VectorWorks 12.5 and 2008.
Create a site model.
￼Trace over the site boundary, or some other shape that you want to use as a boundary.
Cut the shape that you want to use.
Select the Site model.
￼Go to the Menu Bar.
Choose Modify > Edit Group.
At this point you can see all the 3D loci used to create the site model.
Go to the Menu Bar.
Choose Edit > Paste in Place.
Click on the Orange button at the top right of the screen to exit.
￼You are back at the site model. The site model does not show your boundary yet.
Go to the Object Info Palette.
￼Click on the Update button to see the site model stopping at the boundary.