scalar( @$foo )-1

Use $#$foo instead, or $#{$foo}.
By the way, why not iterate over the array itself? for (@$foo) { do something with $_ }

my $i = my $aref = ();

You assign an empty list to two scalars, which isn't quite useful. Consider using just my ($i, $aref);. If you want $aref to be a reference to an empty array, use my $aref = [].

$aref = @$foo;

Makes no sense. This just assigns the number of elements in @$foo to $aref. You don't need a copy by the way. I suggest a rewrite of the loop:

for (@$STF1){
    print OUTPUT "<li>$_->[0]</li>" .
                 qq{<a href="$_->[1]$STF3_Tables">$_->[2]</a><br />\n}
+;
}
[download]

Or a lot easier using printf:

for (@STF1){
    printf OUTPUT "<li>%s</li>" .
                  qq{<a href="%s$STF3_Tables">%s</a><br />\n},
                  @$_;
}
[download]

You have a lot of temporary variables that aren't needed.

# my @temp = foo; my $ref = [ @temp ];
my $ref = [ foo ];
# ($a, $b) = \(@a, @b); return $a, $b;
return \(@a, @b);
[download]

I personally dislike things like // and do { ... } and prefer a simple if (//) { ... }.

Hope this helps...

2;0 juerd@ouranos:~$ perl -e'undef christmas'
Segmentation fault
2;139 juerd@ouranos:~$
[download]