3 options:
Use the cut geometry tool to trim off the end.
If the beams are steel, you should be able to use the coping tool.
If you're using r2008, you could also sketch a beam opening at the end of the beam.
However, I would be suspicious of the fact that the beam and the column are not joining. Steel Beams should automatically cut back from their supporting column if they are joined. Concrete beams and columns should not cut back, but the beam geometry should be cut from the column geometry.
You may want to look into how accurately the structure is modeled, and make sure that end of the the beam lines are coincident with the columns.
Joe