pdfscissors is a good suggestion. A similar application that you can use without the need of an internet connection is Briss
. Try both and decide.
By the way, what I often do is to break each column into two sections (i.e. each page into four sections) so that you can comfortably read them in portrait mode.
Alternatively you could break the document into columns and send them for conversion to your kindle email address. That's probably your best bet if we're talking about the CFR here.