I'm assuming that the underside of the top, and the top-side of the base, are flat, and that the column is rectangular, made up of vertical boards joined in a rectangular cross-section. You want to have vertical dominoes joining the top to the column and the base to the column.
I would position the column on the upside-down top, centered. With pins or double-sided tape, fasten cleats (~20mm x ~20mm) to the top, around the column, snug against the column. Mark each cleat for a domino in the center of each cleat. Transfer that mark onto the face of the column. Remove the column, leaving the cleats, and transfer the mark from the column's face to its end.
To mortise the top, use the joiner vertically against the cleat, aligning the center scribe mark on its base with the mark on the cleat. The inside surface of the cleat will be your reference plane, which is the same as the vertical surface of the column.
Clamp the column flat on the bench. Place the joiner's nose against it, aligned with the end mark, and flat on the bench. The column and the joiner will use the bench as a common reference.
Do the same process for the column and the base. Doing the top joint first will allow you to mess up and hide it more easily. Then you can do the bottom joint right.
This does away with any measuring, almost always a good thing with dominoes. If the design of the column is such that you can't fit the joiner in its end's footprint, you may have to do the cleats a pair at a time, and you will have to ensure that the column's placement is repeatable.
Good luck!
Crox
