does your scanner software have a "Scan Preview" option, usualy a preview option scans at a low res mode, and allows you to select the area you wish to scan. my LexMark X83 has a scan preview and i can tell it what to scan and what to ignore.
There should be - along with that marquee ability, a bunch of controls to allow you to set the DPI, type of photo, Moire reduction and other stuff as well.
Always pays to RTFM.
Note: 72 or 96 DPI is "actual size" depending on the pixel density of your monitor. 300 or 600 DPI is print quality.