I am a big fan of this site and John has given permission for the below to be reproduced here. Enjoy.
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The Treks
by John Bartlett (trekkingeasttimor.org)
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1. Mount Matebean Mane and Mount Matebean Feto

This range is an isolated limestone formation about 20 kilometres south-east of Baucau. It is the birthplace of rivers that flow to the south and north coast,and possibly the most rugged high mountains in Timor.

The trekking is medium to hard and could be done as a two or three-day walk, or separate one-day walks with an overnight stay in the high mountain village of Uaiboro.

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2. Ramelau Mountain Circuit The Ramelau range is the roof of central Timor. There is 4WD (four wheel drive) and truck access to the 1900 metre high village of Hatobuilico and from there you can start the trek over Mount Tatamailau. (At 2986 metres this is the country’s highest mountain.)The trek is then along the spine of the Ramelau mountains and down to the town of Ainaro. A short bus trip and then a walk up completes the circuit back to Hatobuilico.

This medium to hard walk involves one night in a bush camp and one night in Ainaro.

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3. Oecussi Enclave

Oecussi enclave is an extremely isolated and tranquil part of East Timor. This three-day trek starts from Oecussi town on the north coast, an overnight ferry trip west of Dili. It’s a medium to hard hike with one night in the village of Cutete and one night camping. The land borders are all to Indonesian West Timor.

You will need to spend the first night or two after arrival in Oecussi town to organise a guide. The hike goes up the main water catchment valley and over the rugged broken coastal range to stay in Cutete.

Then travel east behind the coastal range to a very isolated border village and up through rain forest and over a pass amongst incredibly wild mountains, to camp on a beautiful grassy ridge.

The following day walk down beside the frontier river to the coast road. Hike along the beach or catch a bus back to Oecussi town.

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4. Atauro Island

Atauro is a four-hour ferry trip north of Dili. The night before the trek can be spent at the beautiful eco resort of  Tua Koin in Villa, or Barry’s Place in Beloi where the ferry docks. The three-day trek is of medium difficulty with two short hard sections. These sections could be avoided.

The walk climbs up and through village gardens and steeply up into the rain forest and then along the spine of the island to the highest point, Mount Manucoco. This steep mountain is visible from Dili. Then west into a rich agricultural area, up to the isolated northern hills and back down to the east coast.

With only a few motor vehicles on the island which are mostly used on the short east coast road, it is a very peaceful place. On the first night of the trek you can camp in the mountains, the second night camp or possibly arrange a village stay.

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Check out John’s site at trekkingeasttimor.org for full details of each of the above treks