Use binmode on your file handle. That will prevent LF from being transformed into CRLF.

Update:

Syntax example (using open syntax introduced in Perl 5.6.0):

open(my $fh, '>', file);
binmode($fh);
print $fh ...
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Alternate syntax example (using open syntax introduced in Perl 5.8.0):

require v5.8.0;
open($fh, '>:raw', file);
print $fh ...
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It works on STDOUT too:

binmode(STDOUT);
print ...
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