Atoms cannot be seen in visible light because they are too small to reflect light in the visible frequency range. The wavelength of visible light is too long to meaningfully interact with atoms, so it cannot be bounced back to an observer in a coherent way.
In order for an object to be visible, light must be able to bounce off its surface. Objects smaller than the natural wavelength of the light being used to scan them are invisible, as they allow the larger waves of low-frequency light to pass through them without bouncing back to an observer. Visible light has a wavelength of between 380 nanometers for violet and 740 nanometers for red. This means that the smallest object that can be perceived in red light must be larger than 740 nanometers across and that the smallest object that can be seen in violet must be no less than 380 nanometers across.
A typical carbon atom has an atomic diameter of 0.22 nanometers. Thus, a single atom of carbon would have to be 1,727 times larger than it is to block a single photon of violet light, and it would have to be 3,364 times larger to be seen in the red wavelength.