When i run your code on my file:

hostname3 # this is a comment for hostname3
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I get:

Use of uninitialized value in substitution (s///) at ./comment line 11
+, <FH> line 1.
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my full code is:

#!/usr/bin/perl -w

use strict;

open(FH, "comments.txt")
  or die "cant open file";

while (my $line = <FH>) {
    chomp $line;
    next if $line =~ /^$/;
    $line = s/\s*\#.*//;
    print "|$line|\n";
}

close(FH);
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humbly -c