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sub Prefix {
  my ($m,$n) = (sort @_)[0,-1];
...
  my $len= length( ( $dif =~ /^(\0*)/ )[0] );
  substr( $m, 0,$len );
}

use Benchmark;
@files = qw(model4run1 model2run1 model4run2);
...
Benchmark: timing 100000 iterations of Jenda, antirice...
     Jenda:  1 wallclock secs ( 0.82 usr +  0.00 sys =  0.82 CPU) @ 12
+1904.76/s (n=100000)
  antirice:  1 wallclock secs ( 0.75 usr +  0.00 sys =  0.75 CPU) @ 13
+3333.33/s (n=100000)