You're assigning each line of the file to @line, when you split, clobbering whatever was there from the previous iteration of the loop. For a matrix the best structure is probably an array of arrays. See perldsc for information on how to go about it. I'd modify your loop to something like this:

my @matrix;
foreach my $line(@filecontents) {
    chomp $line;
    push @matrix, [ split /\s+/, $line ];
}
[download]

That will give you a structure that looks like this. (Per Data::Dumper):

$VAR1 = [
          [
            '0',
            '48.23',
            '17.90'
          ],
          [
            '48.23',
            '0',
            '49.58'
          ],
          [
            '17.90',
            '49.58',
            '0'
          ],
          [
            '59.62',
            '52.04',
            '65.80'
          ],
          [
            '62.20',
            '56.02',
            '68.82'
          ],
          [
            '35.37',
            '37.87',
            '36.52'
          ],
          [
            '27.33',
            '50.73',
            '31.85'
          ]
        ];
[download]

Update: Oops, should have paid closer attention. Looks like you want to split on whitespace, not commas. I fixed the split and data dump.

There are also lots of CPAN modules for doing matrix math which you may want to look at. Check out Math::MatrixReal.