You can use a marquee to define a region to display in the 3D window - (Thin marquee = current storey only, thick marquee = all stories) then "Show selection / marquee in 3D" (F4).
There is also the "Filter elements in 3D" setting, under View > Elements in 3D View menu, where you can limit which stories and/or elements you wish to see.
This is assuming you're using AC11. Previous versions have menus structured differently.