Also, most of the islands are not masked in the output data, I would just like to confirm if indeed MODIS was not able to capture the land within its resolution of if there is a mask product I can additionally use?
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So, to answer your question, it's better to look at the level 2 data of the region to see whether there is a land mask for the islands. You probably will find the l1/l2 browser a helpful tool: https://oceancolor.gsfc.nasa.gov/cgi/browse.pl?sub=level3&per=CU&day=19507&set=10&ndx=0&mon=19448&sen=amod&rad=0&frc=0&dnm=D@M&prm=SST