what happens during collision at molecular level? When two massive bodies collide we treat them simply by their mass interactions with momentum and energy conservations. Down at the molecular level it must be more like a field particle collision for the particles coming in close contact, why dont we consider all these effects ? Are they included in our equations already ?
 A: No, they are not included because they don't affect our results. In Classical Mechanics we don't worry about what's happening at fundamental level, that's the real of QM/QFT. Note that at fundamental level energy and momentum is still conserved.
If we tried to study a classical collision we would immediately fail, because we would have to do $10^{100^{100}}$ calculations. The reasoning is similar to this answer.
To conclude, if Classical Mechanics works, why change it?
A: At the subatomic level, particles interact with each other by the exchange of virtual particles. These particles happen to be always bosons: Gluons for the strong force, W/Z bosons for the weak force, photons for the electromagnetic force and a hypothesized graviton for gravitation. These processes are described by Quantum Field Theory, to illustrate them we can use Feynman diagrams.
So when two macroscopic bodies collide, there will be a massive exchange of these virtual particles, in this case mostly photons, as the electromagnetic happen to be the most important one in this case. Energy and momentum conservation also holds at the subatomic level.
