Of his own methodology, Descartes writes:
Throughout my writings I have made it clear that my method imitates that of the architect. When an architect wants to build a house which is stable on ground where there is a sandy topsoil over underlying rock, or clay, or some other firm base, he begins by digging out a set of trenches from which he removes the sand, and anything resting on or mixed in with the sand, so that he can lay his foundations on firm soil. In the same way, I began by taking everything that was doubtful and throwing it out, like sand … (Replies 7, AT 7:537) [from http://plato.stanford.edu/entries/descartes-epistemology/#2]
Descartes' method of doubt has two purposes:
1. Eliminate all beliefs that could compromise the possibility of certain knowledge. If any belief is open to doubt, then it makes all other beliefs that rest upon it shaky.
2. Discover a belief or set of beliefs that are beyond all doubt. In removing all beliefs that are open to any kind of doubt, Descartes hopes to be left with indubitable knowledge.
This is why Descartes goes as far as he does in doubting absolutely everything. When he finds a first principle upon which to base the rest of his knowledge he wants to be absolutely certain it is sound.
Descartes' applies this method of doubt to all of his beliefs because if there is even one dubitable belief that escapes his epistemic bulldozer, it threatens the integrity of his beliefs' foundations. To switch analogies for a minute, think about your collection of beliefs as a basket of apples:
Suppose [a person] had a basket full of apples and, being worried that some of the apples were rotten, wanted to take out the rotten ones to prevent the rot spreading. How would he proceed? Would he not begin by tipping the whole lot out of the basket? And would not the next step be to cast his eye over each apple in turn, and pick up and put back in the basket only those he saw to be sound, leaving the others? In just the same way, those who have never philosophized correctly have various opinions in their minds which they have begun to store up since childhood, and which they therefore have reason to believe may in many cases be false. They then attempt to separate the false beliefs from the others, so as to prevent their contaminating the rest and making the whole lot uncertain. Now the best way they can accomplish this is to reject all their beliefs together in one go, as if they were all uncertain and false. They can then go over each belief in turn and re-adopt only those which they recognize to be true and indubitable. (Replies 7, AT 7:481)
There are two different skeptical arguments (or epistemic bulldozers) that Descartes uses to raze his dubious beliefs and construct a firm foundation for knowledge.
1. Dreaming Doubt: Rests on the assumption of some degree of similarity between dreaming and waking life. This denies only that there is indubitable certainty that one is awake, because it is conceivable that one could be having a lucid dream identical with waking. This holds even though one might very well be awake.
2. Evil Genius: The dreaming doubt demolishes the certainty of beliefs based on sensory experience, but that still leaves other beliefs that are dubious. This could be described as the "What if I'm just a mind in a vat/matrix?" doubt. But this doubt goes further, in that it stands to undermine the certainty of even the most basic logical and mathematical truths. For the Evil Genius could cause us to be deceived about even these things.

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