The simplest way to do this can be:

use strict;
use warnings;

my @AoA;

while(<STREAM>){

chomp;
next if (/METHOD/);
push @AoA, [split /\s+/];

}

print \@AoA;

__DATA__
METHOD        0TM        1TM        2TM        >2TM
method1        3        68        18        10
method2        3        80        10        6
method3        3        87        9        1
method4        5        83        9        3
method5        6        75        15        4
method6        14        77        6        3
method7        12        82        2        3
method8        9        84        3        3
method9        13        68        16        3
method10    5        65        20        9
method11    9        64        20        7
method12    5        68        18        9
method13    6        82        9        2
method14    11        79        8        2
method15    6        69        20        5
method16    5        80        11        3
method17    1        68        17        14
[download]

What happens here is, the split "tokenizes" each line assuming the space between the words as the delimiter. The square brackets around the split create a reference to an anonymous array which is pushed into the array of arrays data structure.

UPDATE

Umm 2teez already said what I wrote above... I did not check the replies before posting... mesa bad.