I would like to extract data from boxes the coordinates of which are determined by me. I know there is a an option under FUNCTIONS->READ AND PROFILE and then 'Options for box data' but the largest choice in boxes for the latter is only 15x15  and this is still too small for me. Is there anything else that I can do?
Thanks

You have a couple of options, depending on what exactly you'd like to do ...

If you want the data output as ascii text, try functions->output->data->ascii.  Output may be limited by lat and lon coordinates.  Binary output requires knowledge of the start/end pixel/line numbers.  You might also experiment with the blotch function (warning: slightly more cumbersome for this task, but very useful), at functions->annotate/blotch.  If you want to extract the data to a new hdf file, try display->subscene (from the SeaDAS Main Menu). 

Note, all of the above may also be accomplished from the command line, or in a batch file. 

Hope this gets you started.