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for(my $i = 0; $i < @filecontents; $i++)
{
...
    # 
    @line = split(/\,/, $filecontents[$i]);
    # XXX           ^------ do you really mean comma?

    # [] constructs an anonymous array, so we use that.
    # several ways to do it - choose any (not all :-)
...
    # the array @matrix
    push(@matrix, [split(/\s+/, $filecontents[$i])]); 
}

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

#!/usr/bin/perl

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

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

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