I need some help in georegistering the L2 MODIS(Aqua) LAC data.  I have used the HEG tool sucessfully on L2 data from GES DAAC but this utility does not work for the MODIS LAC data obtained through the new SeaWifs browser.  Can anyone shed some light on this subject?

A tool that will allow you to work with the data is SeaDAS, which is available here:

http://seadas.gsfc.nasa.gov/

You can download the version that is available there now and begin utilizing it for your purposes, but a new version (4.5) is soon to be released. It will have new features such as the capability to process MODIS Aqua data from Level 1A to Level 1B, and from Level 1B to Level 2.  It will also provide the capability to create geolocation files from Level 1A files.  The initial release will support RedHat Linux 7.3 platforms, followed closely by support for Solaris and Irix platforms.