perl -ple's/^(\S+\s+\S+).*/$1/' infile > outfile
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perl -ple's/^\S+\s+\S+\K//' infile > outfile
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perl -ne'print if $.>1'
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Update: ah, you don't want to lose the extra columns, oops!

chomp( my $header = <> );
my @headers = $header =~ /\S+/g;

my @fhs;
for (@headers) {
    my $qfn = "$_.dat";
    open(my $fh, '>', $qfn)
        or die("Can't create file \"$qfn\": $!\n");
    push @fhs, $fh;
}

while (<>) {
    chomp;
    my @fields = split(/\s+/, $_);
    for (0..$#fhs) {
        printf({ $fhs[$_] } "%s %s\n",
            $fields[$_*2 + 0],
            $fields[$_*2 + 1],
        );
    }
}
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