You can anchor the regex to the end of the string with $. See perlrequick, perlretut, and perlre. Note the /r modifier I'm using is only available in Perl 5.14 (from 2011) and up.

$ perl -le 'print for map { s/\.(\d+)$/($1)/r } qw/cat.1 ld.so.conf.5 
+/'
cat(1)
ld.so.conf(5)
[download]

Update: See also Re: How to ask better questions using Test::More and sample data