Have a look at strict and the error messages may start to make a little more sense.

You need to declare your variables.

One way could be:

#! /usr/bin/perl -w

use diagnostics;
use strict;
use Getopt::Std;
use Crypt::CBC;

my %opts;
getopt( 'kio', \%opts );

my $cipher = Crypt::CBC->new(
    -key    => '$opts{"k"}',
    -cipher => 'Skipjack',
);
my $INFILE  = %opts{"i"};
my $OUTFILE = %opts{"o"};
open < INFILE  or die "can't open $INFILE: $!";
open > OUTFILE or die "can't open $OUTFILE: $!";
my $plaintext;
read INFILE, $plaintext;
my $chipertext = $cipher->encrypt($plaintext);
print OUTFILE, $chipertext;
close OUTFILE;
close INFILE;
return (0);
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untested