What do u want to prototype exactly?

Every discipline or area of research has its own prototyping tools/equipment.

Dear Sir,

First of all Thanks for your words here.

I'm interested to know only about the generalized and holistic way which can be used in any kind of research activity.

Have a good day !!

I m really not sure how to precisely answer your question since its too general, however this wiki link might give u a hint of what u r looking for....Good Luck

http://en.wikipedia.org/wiki/Prototype

If you are interested in verification and validation of a software prototype, then I would recommend test-driven development. It is very popular in the computer science community as a rapid and rigorous development method.

Check out the wiki page:

http://en.wikipedia.org/wiki/Test-driven_development

Dear Kundan, Prototype differs from a simple to a complex system and hence test differs. Test a two input gate is simple but to test a module of billions gate and 1024 inputs are impossible. Then apply another technique.