How could I achieve that efficiently ? With a 2 dimensional-array ?

Yes, if you don't want to store the entire list of files for final sorting, you can incrementally update an array (or, more precisely, an AoA) that just keeps the n biggest files.   That is, for every file (in your scanfile routine), you'd do

    push @biggest, [$name, $size];
    @biggest = sort {$a->[1] <=> $b->[1]} @biggest;
    shift @biggest if @biggest > $n;  # remove smallest
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You'll be doing quite a lot of sorting, but if the n is reasonably small, those would be small lists only, so this shouldn't be a performance problem.  Also, there are ways to optimize this to avoid unnecessary sorting, but I'll leave this as an exercise...