use warnings;
use strict;

my $user_defined_string = "There's more than one way to do it (more than one).";
my $user_defined_search = '(more)(.*?)(one)';
my $user_defined_replace = '<b>$1</b>$2<b>$3</b>';

my (@subs) = $user_defined_string =~ /$user_defined_search/;
for my $sub (1..@subs) {
  $user_defined_replace =~ s/\$$sub/$subs[$sub-1]/ge;
}

print "mangled replace: $user_defined_replace\n";
$user_defined_string =~ s/$user_defined_search/$user_defined_replace/ge;
print "after: $user_defined_string\n";

__OUTPUT__

mangled replace: <b>more</b> than <b>one</b>
after: There's <b>more</b> than <b>one</b> way to do it (<b>more</b> than <b>one</b>).