Have at it! Just model a wall under the stair and place it on a layer that is not visible in your Floor Plan layer combination. I recommend creating a 'Model Elements' layer for situations such as this!
It does depend on how you made you stair though. If you created your stair with a standard AC library stair, or manually out of basic elements (ie. slabs, roofs, etc), then you can use Solid Element Operations to trim the top of the wall using 'Subtraction with Upwards Extrusion'.
However if you use a StairMaker stair (the ones created using the 'Create New Stair' in the Stair tool), Solid Element Operations won't work. This is a current bug and GS is aware of it - FWIW. In this case you'll need to place a temporary roof aligned with the underside of your stair and trim your wall to it, using the Edit>Trim to Roof... command.
And yes you can create just about anything in the 3D window. Some of the best ArchiCAD users I've met do most of their modeling this way!
Cheers,
Link.