I visited the reserved zone of Manu for 2 days and the trip from Cusco included in total 7 days/ 6 nights. The programme of most tour operators is similar so there is no need to describe it in detail here. You can just check the websites. We drove by transporter from Cusco to Atalaya and then by boat up to Casa Matchiguenka which is one of few of the current lodging options in the real WHS part/ core zone. We booked with Bonanza tours and the tour was operated by Amazon Wildlife Experience which is run by the brother of the owner of Bonanza. So it was the same as with Bonanza only that they laid acquired customers together. We were 8 tourists, one guide, one cook and either a driver or a captain and his boat assistant. The real price was 1290 USD p.P. but as we went to the office in Calle Suecia in Cusco end of August and were flexible and negotiated we could book the same tour for the 14th of September for 750 USD p.P.. Some in our group booked only 6 days and there was not much difference. You don´t miss out on anything only that after a long day you drive all the way back to Cusco instead of staying another night close to Atalaya port and some more bird and monkey watching in the cloud forest. Also a good option to save money. 
 
Maybe good to mention that we almost had a huge accident. Our metal boat with roof with 8 tourists and 5 staff people on board had a motor issue right after the start on Río Madre de Díos close to Atalaya. The river is huge even in the lowest water level month of September and suitable for rafting. The connection between the brand new motor and the tank broke down, so that the motor didn´t have fuel anymore. By this we were left with the river and only had 2 paddles for the guide and the boat assistant to keep control which was not sufficient. First a huge palm tree hit the boat and could have stabbed someone. Afterwards we hit with the long side of the boat a rock wall and almost sunk as the water almost ran on the opposite site into the boat due to the hard hit. Everyone was ready to swim and sacrifice all equipment. We were lacking one life vest. Luckily we didn´t sink, could navigate to the next beach with the current and fix the connection between motor and tank. However before we had 5 minutes of horror and in my opinion unsufficient security measures even though it was more than none. More paddles and maybe an alternative navigation option might be helpful in the boat. 
 
The trip was amazing as Manu is full of wildlife and nice jungle flora. Especially bird enthusiasts will love it. We've been to PN Madidi in Bolivia before and it was quite similar. Unique was the clay licks in Manu where the animals obtain minerals from the soil. We watched the Tapirs at night doing that after a walk through the forest at Bonanza Reserve and the butterflies and monkeys at daytime along the riverbanks. Also close to the Casa Matchiguenka there is a clay lick in the forest were the macaws feed at lunchtime. They're really careful and are easily scared away by humans. After two hours of slow approaching they were finally on the wall for a short time. Special are also the giant otters in Colcha Salvador next to Casa Matchiguenka. We saw one from the catamaran with paddles in the lake how it was first chased by a caiman and then caught a fish and ate it at the shore. Also some of our group saw the silhouette of a jaguar in the morning along the banks of Río Manu but the sun was unfortunately blinding us and then it disappeared. At night many exciting insects, frogs and spiders can be seen. On the drive to Manu one passes through cloud forest with beautiful birds like the nationsl bird of Peru Cock of the Rock and the colourful Golden Headed Quetzal.  
 
Here is a list of all "big" animals that we saw so mainly mammals, birds and reptiles. Probably a lot of spelling mistakes and Genglish but gives you an idea. The ones in brackets we have only seen without picture: 
 
(Golden Crown Fly Catcher) 
Cinnamon Fly Catcher 
(Blue banded Tucan) 
Golden Headed Quetzal 
Cock of the Rock 
(Dusky Green Oro Pendola) 
(Kolibri) 
Wooley Monkey 
King Vouture 
Verci coloured Barbed 
Brown Capucciner Monkey 
Ruffous crested coquette 
Green Honeycreeper 
Yellow Bellied Dacnis 
Lemon Throated Barbet 
Tarantula Hawk 
Great Poto 
(Faciated Tiger Heron) 
Snowy Ygret 
Heuschrecke 
Tapir 
Capybara 
White Eyed Parakeet 
Green Macaw 
(Chestnut fronted Macaw) 
(Kingfisher) 
(Horn Screamer) 
Cobalt winged parakeet 
Winged Parakeet 
(Black Skimmer) 
Great Black Hawk 
(Anhinga- Snakebird) 
Yellow Side Neck Turtle 
Red Howler Monkey + Albino 
Black Caiman 
(White Wing Swallow) 
Brown Kapuziner Affe 
(Squirrel Monkey) 
Red Rocket Deer 
Horsefly --> sticht schmerzhaft, blutig und ignoriert Insektenspray 
(Screaming Piha) --> Nur gehört. Lieblingssingvogel 
(Orinoco Goose) 
Spider Monkey 
(White fronted Kapuziner Monkey) 
Greater Ani 
(Red Cup Kardinal) 
Hoatzin (Asthmavogel, Prähistorikal Bird / Stinky Birds) 
Red Cap Kardinal 
Social Fly Catcher 
(Giant Otter) 
(Whute Wing Swallow) 
(Greater Yellow headed Vouture) 
Blue Common Gallinule 
Red and Green Macao 
(Yellow Rump Casseke) 
(BAat Falcon) 
Great Ygrit 
(Streated Heron) 
Giant Otter 
(Rufescent Tiger Herond) 
Long Nose Bat 
Scarlett Macaw 
Red throated Karakara 
Mascovi Duck 
Limquim 
Orinacle Goose 
(Spotted Sandpiper) 
Wood Storch 
Razor Billed Curassow 
(Giant Cowbird) 
(White Caiman) 
(Collared Peccary) 
Blue and Yellow Macaw 
Yellow footed Turtoise 
Nackte Menschen Mashco Piro (oder Calato = nackt) 
Diamante Dorf Yine (oder Piro) Tribe Name der Menschen die mit den Mashco Piro sprechen können 
Creamsome Crested Woodpecker 
(Mealy Parrot) 
(Swift) 
(Blue throated Pipin Guan) 
(Little Blue Heron) 
Red Belly Macaw 
Andean Mott Mott 
(Andean Solitary) 
(Masked Trogon) 
Speckled Face Parrot 
Colubridae Schlange (Chicotillo, Species: Chironius cf. Multiventris Family: Colubridae) 
 
I would recommand bringing good binoculars and cameras for all the wildlife watching. Our group were all young and only brought smartphones, but we could take pics through the telescope of the guide. Binoculars we rented from the agency for 25 /S per day. 
 
We had Revilino as a guide and I can really recommand him. He is experienced, kind, takes care of each individual and the group and has a lot of knowledge. He comes and lives from the jungle in Boca Manu. He speaks very good English and knows many plant and animal names in Spanish, English and Latin. Mainly he knows birds and mammals and reptiles. Also he is really good in spotting animals. 
 
Manu National Park is a fascinating piece of nature in the Amazonian rainforest. However our guide saw it endangered by humans. There is petrol below the surface which makes it industrially interesting and of course loggers want to cut the trees. But also the native people endanger it. The real indigenous are the Mashco Piro which still run naked through the jungle and live as nomads with low contact to people. It's dangerous to meet them as we can not communicate with them. They have already killed two civilised locals on encounters with bow and arrow. Even more dangerous for the forest though are the Matchiguenkas as they as well as the Mashco Piros are allowed to hunt and cut trees in the national park. However they originally came from the mountains/ Cusco region. Now they use their privilege to kill special animals and cut special trees to sell it. The park rangers belong to the same ethnia so they will not stop them. Our guide claimed that it's quite attractive nowadays to be a Matchiguenka. Apparently they finance their rifles etc. by the money from tourism. Also the Mashco Piros will settle down after they have received enough technology from civilised humans and by this harm the park more, thinks our guide. There is already basic trade between them and the natives in Diamante at Río Madre de Díos who can communicate with them. 
 
Manu national park is a beautiful example of rainforest in South America with exciting flora and fauna.