Final answer:
The prefix of the underlined word "under" in the sentence is "under-", which means "below" or "beneath".
Step-by-step explanation:
The prefix of the underlined word "under" in the sentence "the scientist was trying to find the smallest organism under the microscope" is "under". The prefix "under-" means "below" or "beneath". In this sentence, it indicates that the scientist was looking for the smallest organism that was below or beneath the microscope.