$line =~ s/,//g;
# or, another way to get the same result:
$line =~ tr/,//d;

##</code><code>##

@widths = (3,6,9,2,3,2,3,3,1,2,6,39);
# how to break up the original fixed-width data record:
while (<OLD>) {
   my @out = ();
   for my $w (@widths) {
      push @out, substr( $_, 0, $w );  #pull off a record
      $_ = substr( $_, $w );  # remove it from $_
   }
   print NEW join( ",", @out ), "\n";
}
close OLD;
close NEW;

# in a different script now, but with the same values for @widths:
# how to check field widths if/when NEW file has been "corrected"
open( NEW, ... ) # read the formatted data
open( FIXED, ">...) # re-write the old format with new content
while (<NEW>) {
    chomp;
    my $out = "";
    my @val = split /,/;
    die "bad field count at line $.\n" unless (@val == @widths);
    for my $i (0..$#widths) {
       die "bad data at line $., column $i: $val[$i] (not $widths[$i] characters)\n"
           unless ( length( $val[$i] ) == $widths[$i] );
       $out .= $val[$i];
    }
    print FIXED "$out\n";
}