Use the /s regex modifier. It causes '.' to match newline (which it otherwise does not match):

my $str = "abc\ndef";
$str =~ /(b.*e)/;
print "1[$1]\n";    # 1[]   Use of uninitialized value!
$str =~ /(b.*e)/s;
print "2[$1]\n";    # 2[bc\nde]
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Cheers!
David