Question

Why can't we see atom, such as hydrogen helium
etc....

Answer 1

if you mean through an optical microscope, this is because of a property called the diffraction limit which states that the smallest structure that we can see is proportional to the the wavelength of light that we use. For visible light wavelengths this means that we will only be able to resolve structures down to about 200 nanometers.

This is where the power of electron microscopes come in. using wave-particle duality, the wavelength of electrons is much less than that of light (being sub-nanometer, permitting us to "see" atoms in periodic crystals. A recent publication by japanese researchers demonstrated that they were able to "see" individual hydrogen atoms a using Transmision Electron Microscope http://search.japantimes.co.jp/cgi-bin/nn20101105a1.html. Also see the attached image which shows resolution of atoms in a BaTiO3 (barium titanate) single crystal, with a gold top electrode (taken from Saad et al IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency control, vol. 53, (2006).)