for(my $i = 0; $i < @filecontents; $i++)
{

    # place each line in file
    # into another array
    # 
    @line = split(/\,/, $filecontents[$i]);
    # XXX           ^------ do you really mean comma? 

##</code><code>##

    # [] constructs an anonymous array, so we use that.
    # several ways to do it - choose any (not all :-)

    my $anon_array = [];  # gimme an anonymous array and
                          # assign it to $anon_array
    @$anon_array = @line; # assign to the anonymous array 
    push(@matrix, $anon_array);

    # shortcut:
    $anon_array = [ @line ];
    push(@matrix, $anon_array);

    # compacting further: split returns a list, use that
    # to populate an anonymous array on the fly, push that
    # (the SCALAR value which is an array reference) onto
    # the array @matrix
    push(@matrix, [split(/\s+/, $filecontents[$i])]); 
}

##</code><code>##

my @matrix;
while (<INPUT>) {
    chomp; # you forgot that - remove trailing newline char
    push(@matrix, [split]);
}

##</code><code>##

#!/usr/bin/perl

use strict;
my @matrix;

while (<>) {
    chomp; # you forgot that - remove trailing newline char
    push(@matrix, [split]);
}

##</code><code>##

$#ARGV = 0;  # @ARGV now holds only one element (the first at index 0)

##</code><code>##

print $matrix[7]->[4],"\n";