Atom - Atam or Atma -> Meaning that is subtle, can not be seen, and is the essence of every matter, living or non living - the building block of all matter.
This is the basis of Atomic Theory based on the Indian Philosophies of Sankhaya and Vishesha. This what was meant as the word to describe the Soul - which can not be seen and was said the thing that can not be destroyed and survives death. This was the first philosophical musing at the law of conservation of matter and energy - because the (body) matter did generate energy in form of motor locomotion, and other body functions.
Anatomical - An-Atam - meaning that is not subtle and is gross. That is the body and its parts! One adds "an" to make an opposite meaning for words starting with vowels. The same rule is borrowed by English in usuage of articles. To make it adjective - one would add "ic" - which is there in Sanskrit also. So it becomes An-Atom-ic. This makes it like -ness, which is abstract form of adjective attribute. To make it into a concrete adjective noun - one that is with the property of -ness, one would make it by adding "aal", and that becomes "an-atam-ic-al" which got corrupted into "anatomical".
Anatomy - An-Atam-ay - or An-Atam-maya Something that is "an-atomic-full". Double "m" becomes single "m".
We have used only Sanskrit rules to explain these words.