Having read through a number of Descartes works, I am struck by what seems to be a difficulty in his reasoning process. Roughly put his reasoning goes something as follows (please note this is in summary form):
1. Knowledge (science or Truth) is that which is indubitable, being clearly and distinctly perceived.
2. If knowledge is defined as in premise one, then in order to discover truth one simply doubt all that is not indubitable, which is not clearly and distinctly perceived.
3. We can doubt all that we thought we knew, except for one thing, that we are doubting.
4. I doubt, and therefore I exist. (Or in his more famous phrase, I think, therefore I am – Cogito ergo sum)
5. That “I think” is the clearest and most distinct truth I can know.
6. I am aware of imperfections.
7. The fact that I am aware of imperfections seems to necessitate that I have an idea of perfection.
8. This idea of perfection can only come from (a) my own mind, (b) the world that my senses appear to perceive, or (c) from a source that is higher than me.
9. Options (a) and (b) are not possible, because they are the source of imperfection.
10. Therefore my idea of perfection is put in my mind by a higher being.
11. Due to the principles of causality (see The Principles of Philosophy, principle XVIII) this higher being must itself be perfect in every way.
12. Existence (this is presupposed) is a perfection, therefore this being must, necessarily, exist.
13. Therefore, God exists.
14. As perfect, God must also, necessarily, be absolute truth.
15. As absolute truth he could not, in any way, deceive me, make me such that I would always deceive myself, or be the cause of the errors that I perceive in my sense and thoughts.
16. Therefore, whatever I perceive clearly and distinctly is true.
17. Therefore premises 4 – 15 are necessarily true (because they are clear and distinct ideas, or deduced necessarily from clear and distinct ideas).
This is a rough draft, summarized, and not worked out so as to ensure its logical perfection. It is a summary of Descartes reasoning process. The main points are there. The problem that I see in it is two-fold: (1) What about the definition of knowledge as that which is indubitable, being clearly and distinctly perceived? Is this definition itself indubitable, being clearly and distinctly perceived? (2) What about the methodical doubt, is it clear and distinct, that this method is, without a doubt, necessary for discovering truth? If the answer to either of the above questions is “No!”, then, or so it seems to me, Descartes whole system is fallacious. 
I am aware that this critique of Descartes may be found elsewhere, however, these are my humble reflections after having read through Descartes Rules for Direction, Discourse on Method, Meditations on First Philosophy, and part of his Principles of Philosophy. I am open to correction, and if anyone has read a similar critique in a book I would appreciate a reference.