How about:

use Data::Dumper;
my @uris = qw(
   http://www.foo.bar/index.html
   http://www.foo.bar/index.html#foo
   http://www.foo.bar/index.html#bar
);

my %seen;
my @unique_uris = grep !$seen{$_}++, map /^([^?#]+)/, @uris;
print Dumper(\@unique_uris);
[download]

That would catch everything to the left of a # (anchor) and ? (query) character (if there is one), which I believe is what you want.

Hope that helps.