A careful reading of a manuscript is one of the most important elements of a critique. I like to read a work at least three times (length and time permitting, and not necessarily at the same sitting), and live with it for a few days. I am always struck by ideas that come to me after some time away from the initial reading. The mind needs to "digest" what it has read, and is then better able to make creative connections, observations, etc.
I approach a manuscript in three basic steps: I look first at its overall structural development (are the ideas consistent and flowing?), then I approach it line-by-line (are the sentences sound grammatically, and how well do they relate to one another), and finally, copyediting (are words spelled correctly, punctuation correct, and facts accurate?).
While my approach to critiquing a manuscript is not a strict 1,2,3 approach, but oftentimes, more like an organic blend of the three, it's still good to think in terms of these steps because they are the basic elements of a thorough critique.
Though it is good to start out with pen in hand to mark a manuscript with whatever first impressions catch the eye, always read a
work more than once for the kind of insight that produces a valuable critique.