If the cloud information is not important for your analysis, then u can overlay two MODIS images of similar area, but taken in different season i.e. cloud free + image with cloud

Thanks for suggestion.

Cloud information is not necessary for our analysis if did different season image the result will become wrong because we want to do only kharif season for yield estimation.

Dear Sanjay Kumar

In the books of each of the MODIS products (search Ej "MOD11 ATBD" O "MOD13 ATBD") you will find the algorithms used for the generation of the images of compound days, which already have corrections for the presence of clouds

The following link: https://lpdaac.usgs.gov/documents/104/MOD13_ATBD.pdf

corresponds to vegetation indices:

" 3.2.6 MODIS VI composite algorithm The logic of the compositing algorithm is based on the MODIS specific input data and theoretical knowledge of radiative transfer and surface reflectance anisotropy. The compositing algorithm will optimize the choice of the best VI representative for each 44 composite period, spatial resolution and global land extent. The compositing algorithms will rely on information from the cloud mask (Ackerman et al., 1996), atmospheric correction (Vermote, 1997a), view zenith angle, solar zenith angle, relative azimuth angle, geo-registration (Wolfe et al., 1998), and surface BRDF normalization. The algorithms utilize the information in the reflectance-quality assurance (QA) flags, partially derived from the MODIS cloud mask product, to pre-process the atmospherically corrected reflectance data of MODIS bands 1, 2, and 3 and 7 (red, NIR, blue, MIR) over land only. Land pixels with clouds, shadow, and bad data integrity will be excluded from the VI composite. The MODIS algorithm selects all the reflectance data for a 16-day period, based on data integrity and cloud flags, and fits the Walthall BRDF model to the individual band data. The empirical BRDF model developed by Walthall et al. (1985), is used to derive nadir reflectance data for each pixel and 16-day intervals"

Regards