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The best-suited scientific instrument for mapping the ocean floor is sonar. Sonar, which stands for Sound Navigation and Ranging, uses sound waves to detect and locate objects underwater. It works by emitting sound pulses and measuring the time it takes for these pulses to bounce back from the ocean floor or other submerged objects. This allows researchers to create detailed maps of the seafloor topography, providing crucial data about underwater features such as mountains, valleys, and flat plains.

In contrast, a microscope is primarily designed for magnifying small objects or details at a microscopic level, which does not apply to vast ocean floor mapping. A seismograph is used to measure and record seismic waves and is more relevant in studying earthquakes and geological activity, not the ocean floor's geography. A thermometer measures temperature, which is important for oceanography but does not contribute to mapping the physical structure of the ocean floor itself. Thus, sonar is uniquely equipped for this specific task, making it the ideal choice for such applications.