Instead of using explicit while(){} and for(){} loops, I tend to use perl's built-in looping constructs.

# read
use Path::Tiny;
my @words = ( path($filename)->slurp ) =~ /^.+$/gm;
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or

# optional read without Path::Tiny
my @words = do { local(@ARGV, $/) = $filename; <> =~ /^.+$/gm };

# or
my @words = do { local(@ARGV, $/) = $filename; split /\n/, <> };
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and for write

# write
use Path::Tiny;
use List::Util qw( uniq );
path($filename)->spew(join "\n", uniq(@words), '');
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The regex on input was a win for me reading /usr/share/dict/words on my system which has over 123,000 lines in it.

General rule: Don't do things item by item when you can do multiple things at once.