An atom is an unbelievably small “object”. To even call it one is straining the definition of what an object is.
The first thing to understand is that to “see” something, light must be able to bounce off it and get to your eye and your optic nerve. The wavelength of visible light is about ten thousand times the diameter of an atom, so there’s no way to actually perceive an individual atom- they’re just too small.
When atoms are arranged into molecules, those molecules can then be arranged into material that becomes large enough to interact with light waves in a meaningful way, so light can reflect off it and bounce back to your eye and optic nerve.
Some materials can be transparent to certain wavelengths of light- like glass, or the lens in your eye, so when light at specific frequencies encounters such material, it simply passes through unhindered.
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