For a trip of about three weeks, you could follow this itinerary: Lima, Nazca, Huacachina, Arequipa, Colca Canyon, Puno, Cusco, and the Jungle (Madre de Dios or Manu), then back to Cusco. Optionally, you could travel from Cusco back to Puno and continue by bus to La Paz (Bolivia). We have also written a detailed article about this.
If you have specific questions about your route, please get in touch with us.