on one page I mark and point my rectangle and use this command ctr+x+r+d to delete the marked rectangle
if the rectangle is spread on 2 pages and more i can't able to mark and point the rectangle could someone provide how i mark and point rectangle longer than one page (one screen)
You can set the mark with C-SPC. Then you can move the point to wherever you want (including several pages down) and delete the rectangle with C-x r d, the mark does not have to be displayed to work - see http://www.gnu.org/software/emacs/manual/html_node/emacs/Setting-Mark.html .
Perhaps you would find it useful to use M-x transient-mark-mode - which visually depicts the region by highlighting it.
Why can't you select a larger rectangle? Doesn't your emacs auto-scroll when you drag the selection below the lowest line?
Anyway, alternatively you can just type Ctrl-space, move to where you want with the keyboard, and then use Ctrl-x r d.
You should certainly be able to delete a rectangle spanning multiple pages of your buffer, as others have already said. I'm not sure what the issue is there.
I just thought I'd point out a useful alternative, which is provided by cua-selection-mode, and which highlights the rectangle you are manipulating. Trey Jackson made a handy blog about it which shows all the documentation (or look in the source file, which is cua-base.el).
Place (cua-selection-mode 1) into your .emacs and then you can toggle the rectangle editing mode on and off with C-RET. When it's on, move point to drag out the rectangle. DEL will delete the rectangle, and C-w will kill it if you want to be able to yank it back.