This website is grouped per region, so you can easily find places to visit that are close to each-other. Links in bold are the places that in my opinion should not be missed. See here for all the other regions. Click here for hiking in Macedonia and general information about Macedonia.
The west side of Lake Prespa: Stenje, Konjsko and the uninhabited island Golem Grad (a.k.a. Snake Island).
The east side of Lake Prespa: Podmocani, Kurbinovo, Slivnica, Nakolec, Ljubojno and Brajcino.
My Macedonia Blog 