foreach ($lines) {
    $lines = ~ s/(?<=,)([^,]*),/\1/g;
    print("$lines \n");
}
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In addition to the fact that the scalar  $linesdoesn't appear to be defined anywhere (you are using warnings and strictures, aren't you?), the statement
    $lines = ~ s/(?<=,)([^,]*),/\1/g;
should probably be
    $lines =~ s/(?<=,)([^,]*),/$1 /g;
(the  =~ operator should have no space between = and ~, use  $1 instead of  \1 in the replacement string, there should actually be a space somewhere in the replacement string if you want to replace a ',' with a space). I would suggest something like (untested):

foreach my $line (@lines) {
    $line =~ s/(?<=,)([^,]*),/$1 /g;
    print("$line \n");
    }
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Update: After further inspection of the OP and replies, it appears that rohanan wants every ',' after the first replaced with the empty string rather than with a space. So (still untested):
    $line =~ s/(?<=,)([^,]*),/$1/g;