Scientists "see" things through specialized equipment that identify waves that are invisible to a human eye i.e. microwaves, gamma waves, etc.
Black holes don't give off gamma rays or microwaves. That's the whole point. (Except hawking radiation, of course, but that is hard to detect as the effect is so small in large objects.)
Seeing objects that don't reflect light is tricky business. And black holes are as mysterious as a target can be. Not even light can escape them. This is a pretty tricky problem for scientists, whose instruments usually rely on light-- whether it's visible light, radio waves, X-rays or infrared-- to observe objects in space.
One method to see black holes has been to watch the fate of an object falling into one of these cosmic graves. If material actually falls into a black hole, it gets shredded apart and it heats up. As it heats up, it starts emitting light and this radiation we can observe. In particular, we can often see X-rays coming from black holes. When gas orbits around a black hole it tends to get very hot because of friction. It starts emitting X-rays and radio waves. So a lot of times black holes can be found and studied by looking for bright sources of X-rays and radio waves in the sky.
These X-rays do not get through the Earth's atmosphere and can only be seen with telescopes positioned in space, such as the Hubble telescope.
The strong gravitational attraction of a black hole affects the motion of nearby objects. When astronomers see a star circling around something, but they cannot see what that something is, they may suspect it is a black hole. Astronomers can even figure the mass of a black hole by measuring the mass of the star and its speed. The same kind of calculation can be done with black holes at the center of many galaxies, including our own galaxy, the Milky Way. In fact, at the very center of our galaxy, radio and X-ray telescopes have detected a powerful source called 'Sagittarius A', identified as this massive black hole.