Then assuming nothing else is referencing parts of the data structure held on to by $word_index_ref, all you need do is:

$word_index_ref = undef;
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at which point perl will release all the memory allocated to $word_index_ref back to its heap where the memory will be available for reuse. However, do not expect to see the memory footprint for the running Perl application reduce at that point because perl typically does not hand the freed memory back to the OS.

You can let scope do this for you:

{
    my $word_index_ref = retrieve( $word_index_file );
    # Use $word_index_ref here
}
# $word_index_ref is out of scope here
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When the block (scope) in which lexical variable $word_index_ref is declared is exited, the variable goes out of scope and, if there are no remaining references, associated memory is freed. This is one reason for using lexical variables and declaring them in the smallest possible scope. Sometimes an appropriate scope already exists (e.g. the blocks of subroutines, loops and conditionals), but you can create one anywhere.