From Level 2 data file, you can directly see the latitude and longitude over which it contains the MODIS retrievals using e.g. IDL or MATLAB. In case the retrievals are not available directly over your location, you can define a spatial region around your site. 

Dear Narendra,

I have opened the data in hdfview, there are 3 files one is latitude, one is longitude and one is data file, the spreadsheet is having different cells for lat and lon, so how will we come to know that which data is corresponding to my lat/lon

You can also try HDF Explorer  or HDFLook.

http://www.space-research.org/

http://www-loa.univ-lille1.fr/informatique/index.php?lang=us&p=about&app=HDFLook

Hi Manish, 

You can use MODIS Conversion Tool Kit (MCTK) to convert from HDF to GeoTiff and they use any image processing software to view it and select the data for your required particular lat/long. Good luck!