Construct an array of offsets and use substr to delete the unwanted parts.

Update: ... as BrowserUK already suggested....

use warnings;
use strict;
#use Data::Dumper;

my $mask = '0001111111001111001111111';
my @mask;

while ( $mask =~ /0+/g ) {
    push @mask, [ $-[0], ( $+[0] - $-[0] ) ];
}

#print Dumper \@mask;

#print $mask,"\n";

while (my $string = <DATA>){
    #print $string;
    chomp $string;
    for (1..@mask){
        my $replace = ''; #'*' x $mask[-$_][1]; #check to see 
        substr $string, $mask[-$_][0], $mask[-$_][1], $replace; 
    }
    print $string, "\n";
}


__DATA__
0123456789abcdefghijklmnopqrstuvwxyz
0121012102??????????12121212????????
0111011102??????????12111112????????
0111011102??????????12111112????????
[download]

3456789cdefijklmnopqrstuvwxyz
1012102??????12121212????????
1011102??????12111112????????
1011102??????12111112????????
[download]