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 );