I would need to read in the file, encrypt column 1 & 9, then output the file in the same format but with those values having encrypted values.

OK, so it looks like you have some of the framework done. Looking at the Crypt::CBC page on MetaCPAN, you're not encrypting the fields correctly. You need to get each line of the file, split it into fields, encrypt two of the fields, and write the fields out to a new file.

  use autodie;  #  Using this module means open and close errors are
                #  handled nicely.

  my @affected_fields = qw/0 8/;
  ..
  #  Figure out the input and the output file names here ..
  ..
  open ( my $input_fh,  '<', $input_file );
  open ( my $output_fh, '>', $output_file );

  while ( <$input_file> ) {

    my @fields = split ( /,/ );
    if ( $type =~ /^en(crypt)?$/ ) {

      foreach ( @affected_fields ) {

        $fields[ $_ ] = $cipher->encrypt( $fields[ $_ ] );
      }

    } else {  #  I would prefer to use an elsif here, but 
              #  you could catch this during parameter checking.

      foreach ( @affected_fields ) {

        $fields[ $_ ] = $cipher->decrypt( $fields[ $_ ] );
      }
    }

    print $output_fh join (',', @fields ) . "\n";
  }

  close ( $input_fh );
  close ( $output_fh );
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PS, Always, always, ALWAYS use strict and use warnings.