Like this?

use strict;
use warnings;
my $i = 0;
while(<DATA>){
    s/<foo>.*?<\/foo>/"<foo>".++$i."<\/foo>"/e;
    print;
}
__DATA__
<foo>3</foo>
<bar>a</bar>
<foo>14</foo>
<bar>bc</bar>
<foo>159</foo>
<bar>def</bar>
[download]