#! perl -slw
use strict;

open SEQ,  '<', 'data1.dat' or die $!;
open MASK, '<', 'data2.dat' or die $!;

while( my $seq = <SEQ> ) {    ## Read a sequence
    my $mask = <MASK>;        ## And the corresponding mask
    $mask =~ tr[N][ ];        ## Ns => spaces
    print $seq | $mask;       ## bitwise-OR them and print the result 
}
close SEQ;
close MASK;