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Uh?What's it all about chandan?
I think you are talking about changing a Very Large Scale Integrated Circuit - circuit diagram. It may be a change to a circuit containing a VLSI chip (or chips) or a change to the circuit within the chip itself. This is my line of business so if you explain what you want to know I should be able to answer you.
what about using CPLDs?
The topic huge.., and an unending story...
Chandan, you have never actually said what you are trying to do or from what base of knowledge you are starting. I have tried to answer your questions fully without knowing this, but to help further would involve me in researching the web, which you could do equally well. If you have a specific task in mind, then say what it is and I may be able to point you in the right direction. I don't know any free e-books on FIB modification.
If you are thinking of trying your hand on a little 'reverse engineering' here then that seems quite hard Chandan. I think you need advanced machinery to 'scan' the chips layers and then you need to know an awful lot of how the 'logic circuits' can be expected to look. http://en.wikipedia.org/wiki/Microfabrication.Take a look here http://www.flylogic.net/blog/
Chandan, I don't wish to put you off your pursuit, but you seem to be starting from a base of knowing little about this very sophisticated technology and wish to do something "practical". Have you thought about taking a course at a university to study the subject in detail? If you have a degree in physics or electronics (for example) you could probably find a university with suitable facilities to pursue a post-graduate course in this field. There is a good deal of interest in the subject and there may be semiconductor companies or equipment manufacturers who may help fund a research project.