It is possible that a GDSII file may contain in its hierarchy many references to structures that are empty. What is meant by an empty structure?

A structure is empty if:

1. It contains no entities - i.e. boundaries, text or paths

and

2. any SREF's in it refer to structures that are also empty.

So you can see that the definition is recursive ... before you can say a structure is empty you must first check all of the SREF's in it and determine that those point to empty structures ...

Why Prune the Hierarchy Tree?

A large GDSII file may contain a very deep hierachy. Viewing or operating on such a file is time consuming since it involves lots navigating down through the hierarchy. If large parts of the tree are essentially empty then pruning off those branches will make manipulating the file much more efficient.

Command Line Syntax

If you use an operation such as include layers (-i) and you also want to remove any empty branches of the hierarchy tree after the data has been filtered by layer then add the -prune option to the GDSFILT command line.