my @sorted_matrix = grep {s/(^|\D)0+(\d)/$1$2/g,1} sort {$a->[0] cmp $b->[0]} grep {s/
(\d+)/sprintf"%06.6d",$1/ge,1} @matrix;

As it stands, the first  s///ge (with the sprintf) operates on (and destroys) the top-level array reference. It can fairly easily be made to work, but I wouldn't: it makes my skin crawl.