while (<FILE1>){
       chomp;
       my @array1=split;
       my $a1=$array1[1];
       my $a2=$array1[2];
           ......
         while (<FILE2>){   #wrong, cannot iterate all the lines
          my @array2=split;
          my $b1=$array2[0];
          my $b2=$array2[1];
             if ($a1 eq $b1){
        	  .......}
             else {......}
         }
    }