How can we seperate parts of words?
I mean seperating into prefixes suffixes and roots.
For example in word such as "periodic" What is prefix and What is root?
What is the difference between root and affix? Is there any certain border?
For example in "geology" and "geometry" What can we call the term "geo"?
Or in "geology" and "logic" What is the role of "log"?
A good dictionary will tell you the etymology of words you are interested in, for example: geology - Dictionary definition and pronunciation - Yahoo! Education
Context is always important; labelling is rarely important.
This topic in linguistics is called morphology:
Here's a site you can look at, but it's quite advanced. Look elsewhere for "morphology in linguistics". Should find something.
http://en.wikipedia.org/wiki/Morphology_(linguistics)