Hello idlehands, and welcome to the Monastery!

As toolic says, you can remove carriage returns with the substitution operator. The transliteration operator is another option:

$result =~ tr/\r//d;
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But most likely you don’t need backticks at all: forget ls and just use Perl’s built-in commands. For example, to get a list of all the plain files (but not directories) in directory $dir:

use strict;
use warnings;
use autodie;
use Data::Dump;

my $dir = ...;

opendir(my $dh, $dir);
my @f = grep { -f } readdir($dh);
closedir $dh;

dd \@f;
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See readdir and the file test operators.

Hope that helps,