prefixes

[ronak]

How can we know that which prefix we should use with which root word

[svartnik]

Learn the meanings of prefixes and then apply them accordingly.

[Tdol]

If you're referring to negative prefixes, we often don't. there are some rules like im- before a word beginning with P, but these are far from perfect and with the major ones like un/in, it's really a matter of using a dictionary, I'm afraid.