This is clearly not your actual code, not only because of the syntax error in your regexes that tilly pointed out, but also because, if it were your actual code (and the syntax error were fixed), then the second snippet would work.

#!perl

undef $/;
$text = <DATA>;

while ($text =~/foo(.*?)bar/g) {
   manipulate ($1)
}

sub manipulate {
  print "@_\n";
}

__DATA__
foo this is one example bar
this is a line I don't care about
foo here's another keeper! bar
foo yet another bar
and a line to reject
[download]

and the output:

 this is one example 
 here's another keeper! 
 yet another
[download]

Please provide some code, whether it's your original code or a short snippet, that actually demonstrates the problem you are having.