Various embodiments of a system and method for automatically re-arranging a graphical program are described. The method may operate to receive user input excluding a portion of the graphical program from re-arrangement, and to then automatically re-arrange the graphical program without re-arranging the excluded portion of the graphical program. In various embodiments, the objects in the non-excluded part of the may be re-positioned so as to better organize the graphical program or enable a user to more easily view or understand the graphical program.