Can anyone please provide some links(or suggest books) where the MSAA algorithm is clearly explained? I was able to find links where implementation of MSAA was explained from an application’s perspective, not as an algorithm.

http://en.wikipedia.org/wiki/Multisample_anti-aliasing
To sum up, it means only depth is actually supersampled. Each time a there is a single triangle covering a whole pixel, the shader is evaluated only once per final pixel.
Multiple evaluations are only performed for triangle edges and intersections.