Your update underscores a point I like to make. Whenever you can, avoid C style loops in favour of Perl's foreach construction. Thus you would write:

foreach my $i (0..$#line) {
  $record[$row]{$fieldname[$i]}=$line[$i];
}
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The reason is that you will make fewer fencepost errors that way. (One of the most common bugs in C, but generally automatically avoidable in Perl.

Beyond that I would recommend using a -1 for the third argument to split, and given that you have tabular data I would lose the loop entirely for a slice:

my %rec;
@rec{@fields} = split(/,/, $_, -1);
$record[$row] = \%rec;
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(I would actually clean it up even more, more on that in another post.)