I don't have PDL installed, but this should do it:

my $m = [[],[]];

while ( <DATA> )
{
  chomp;

  my @l = split /,\s+/;

  push @{$m->[0]}, $l[0];
  push @{$m->[1]}, $l[1];
}

$m = PDL::Matrix->pdl($m);
__DATA__
0.6490,    0.0330
0.1150,    0.0290
0.0070,    0.3570
0.0630,    0.0760
0,         0.0400
0.0120,    0.0620
0.1530,    0.4020
[download]