There is a way indeed. Your approach doesn't work because tr/// returns the number of transliterations (or in your case, removals), and map collects return values. So you need to actually return $_

use strict;
use warnings;
use Data::Dumper;
$Data::Dumper::Useqq = 1;
my @a = ("a\000b\000c", "foo\000bar");
print Dumper \@a;

my @cleaned = map {tr/\000//d; $_ } @a;
print Dumper \@cleaned;
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Please note that a common cause for null bytes is the use of UTF-16; if that's the case, don't remove the null bytes, but decode the strings.