Does your question refer to the GDSII file storage or to creating a hierarchical design in your layout tool?
As for the GDSII format: cells are stored one after another. There is no "top cell", but you can create a hierachical design by inserting cell instance references ("SREF") into other cells.
In the Calibre DESIGNrev reference manual (calbr_drv_ref.pdf in Calibre's docs directory), see the example in $L create cell -- it sounds similar to what you want.