I ride a 2009 Trek Madone 6.5, and I was wondering if there is anything I should take into consideration when buying a rear bike rack for a carbon frame.

Contact Trek and ask them - they are the experts on their CF frames, and whether they are suitable for attachment of racks to support touring loads.

You have a choice of a seatpost-clamping rack or one using the wheel quick-release and the seatpost collar as mounting points. You can't use P clips on a carbon frame.
Seatpost racks need a beefy metal post so replace the carbon one with a midrange aluminium, nothing ultralight. The racks come with a low max load, maybe two small panniers.
Another alternative is a large Carradice saddlebag, with a barbag up front.