I am currently reading Herman Dooyeweerd's In the Twilight of Western Thought: Studies in the Pretended Autonomy of Philosophical Thought (the subtitle alone is worth the price of the book).  There are so many gems in this book.  Dooyeweerd is attempting to show that modern philosphical thought (in general) pretends to be autonomous and neutral, but is nothing of the sort.  All philosophical thought is ultimately rooted in and driven by some set of religious convictions or axioms.  Dooyeweerd speaks in terms of "ground motives".  Here is Dooyeweerd on the pretended autonomy of Descartes, and the implications of Descartes' project:

"Humanist philosophy eliminated the so-called supra-natural sphere.  Nor would it accept a given world-order founded in divine creation.  This was incompatible with its religious basic-motive which implied the absolute autonomy of human reason.  It could not accept any order of the world that does not originate from from the autonomous and free human reason itself.  Therefore, the Cartesian philosophy started with a methodological, theoretical destruction of the world as it presents itself in the given order of human experience.  After this methodical destruction of the given world, only the thinking human ego with its innate mathematical ideas is left.  And this thinking ego, which seeks the criterion of truth only in itself, sets itself the task of recreating the world in the image of its mathematical pattern of thought" (p. 48)