The bits you have commented out may be more important than many of the bits you left in. Most important (as already mentioned) is that you have commented out the 'use strict;' line. Why?

#my file_ref = (); is an interesting commented line because it doesn't compile uncommented. However later in the code file_ref is used as a hash, although the name suggests a reference to something. Later #my %file_ref; occurs which looks like it's related and compiles correctly uncommented - why is it commented out? Uncommenting the %file_ref declaration fixes the compile error that the use strict line was probably commented out for.

The code you present is not novice code. On the other hand there are large swathes of code missing. Where did the original code come from and how did it get into its current state?

What are the explicit problems that you are having?