Question

Does the fractional snow cover of modis data give exact snow cover area of a watershed

Answer 1

A simple way to get fractional snow cover from MODIS is:

http://neo.sci.gsfc.nasa.gov/view.php?datasetId=MOD10C1_M_SNOW

There you can download this data directly and easily as GEOTIFF or csv.

Also:

Cloud filtering is already done in these MODIS products. A disadvantage of the NEO products from the homepage I suggested to you is of course that best geographical resolution is 0.1° * 0.1°, that means about 10*10 km.