Question is what exactly title says that have we ever seen an atom through any means (microscopes/equipments.etc)? If not, how do we know they exists?
Scanning tunneling microscopes can "see" atoms. Here is a 2008 issue of Nature magazine:
What you're really seeing here is an electrical equipotential surface, which is close enough to being a solid surface for most purposes. A scanning tunneling microscope (or the similar atomic force microscope) is like a very precise phonograph; it traces over a surface and senses the atomic-scale bumps in a surface. It's not too much inference to assume that the atomic-scale bumps are really atoms. The colors are added though; any atom is smaller than a wavelength of visible light.
How did we know atoms existed before that? Well, that's quite a story, and Wikipedia probably tells it better than I can.