In doubting all things, when you try to doubt your own existence, you run into a contradiction, because doubt is a conscious activity. You cannot doubt that you are doubting, and therefore that you exist. What sort of existing thing are you? Descartes immediately discards the scholastic definition of rational animal, and considers the powers often attributed to the soul before discarding most of them as well - nutrition, movement, sense perception, imagination, etc. He settles on thinking: "I am in the strict sense only a thing that thinks." Not a soul, but a mind. "A thing that doubts, understands, affirms, denies, is willing, is unwilling, and also imagines and has sensory perceptions."
This gives us insight into what Descartes means by "clear and distinct." Clear: readily understood, simple, lacking ambiguity. Distinct: separated from other concepts and ideas, non-muddled. An obvious class would be geometrical theorems, but your personal existence as a being which thinks is another example.
Similarly, for all the activities of the mind - sensation, imagination, willing, etc - the same logic of cogito, ergo sum applies, because these activities are all forms of thinking and reduce to it. The list of mental operations could be multiplied indefinitely, but they all have thinking in common, so classifying them all under 'thinking' makes good sense.
To illustrate this point about clarity and distinctness, consider that this definition - a being which thinks - does not really correspond to any mental image, whereas 'tiger' certainly does. The image of a tiger appears to be clear and distinct. Is it? Descartes uses a simpler example - beeswax - but any specific body would do, and testing this same process on any number of different bodies might be a useful exercise.
Wax, like several other bodies - water, oil, air - can take different forms and become very different. What do the forms have in common? Wax is something extended, flexible, and changeable. This judgment is from the mind, not the senses, even though the senses are what relay the observed changes to the mind. This more reflective understanding of the wax is what is clear and distinct, not the multiple, varying perceptions of it. The corollary is that every consideration of the mind towards a thing that helps to understand it, helps also to establish more effectively the nature of the mind.
The conclusion is that bodies are not, strictly speaking, perceived by the senses, but by the intellect alone (note the shift from 'soul' to 'mind'); this perception derives not from their being sensed, but from being understood. And because it is one's mind doing this activity, all of these reflections on bodies further articulate one's own powers of thought.
What actual understanding of bodies has been achieved here? Take the understanding of wax: wax is something extended, flexible, changeable. But so is wood. So is steel. And rubber and wool and countless other bodies. So therefore wax is steel, and all the other bodies as well. But this is absurd. Therefore our understanding of the material world is not understanding which is clear and distinct.
