Ngo, Saif is right - SeaDAS should be able to read the .main files. If that doesn't work, then you have a problem - may the files corrupted on download? If you can load the files into seadas then your next problem is that all the navigation data is wrapped up in the hdf attributes. I usually use a seadas script to output the data I want, and the lat/lon data, into plain hdf files (e.g. 1 file for data, 1 file for lat/lon). These can be read by matlab or similar. You can also convert them into .grd, .nc or other files using GDAL. Let me know if you'd like a seadas script to adapt.
Thank you Mr Jill Schwartz and Mr Saif Uddin. It is very good when seadas script can be use. I would like to try using seadas script but I am not familiar with IDL.I can use Matlab, instead. Could you please suggest some advice or documents about seadas script?
Here's a generic seadas script to read Level 3 SST files and output a patch of the South Pacific out to plain hdf files, which can easily be read in Matlab (see end of script). You need to change the file extenstion to .bat. I'm not sure if that's exactly what you need so do say if there's a problem. Also, the Ocean Color Biology Processing group hosts a brilliant support forum:
oceancolor.gsfc.nasa.gov (right hand side - forum), with a section devoted to seadas questions.