I recently purchased a piece of 16 inch piece of rail as a starter anvil. The rail is rough on both ends and I want to either grind or mill the ends flat. My question is, If I grind it flat, will the heat generated anneal the metal requiring a heat treat or should it be ok afterwords?

Welcome to IFI Crytin,

Take some time to read the info already available, your question has been answered numerous times, if you read the relevent sections you will also find the answers to the questions you don't even know you wanted to ask yet.

Above all, do nothing to your track untill you'e absorbed all the info on rail road track anvils and then you'll realse what you are about to do wrong, before it's too late.

 

I'll give you a few hints as to the information you will find, first, an annealed hunk of rail is better material than was used in 90% of the history of smithing, and is substantially harder than steel at forgot temp. Would heat treet improve it, yes sir but I wouldn't recomend it for a beginner. 

Second, how rough is rough? Are we talking torch cut buy an gorilla, torch cut buy a pro or cut buy a band saw or chop saw? All but the first requires something drastic, but the cheepest for both the torch cuts would be to have some one with a bandsaw cut off the ends square and then clean them up with sanding disk on a 4" grinder. 

From there, use it, modify it, what ever. 

 

Torched pretty roughly on 1 end and sawed off really badly on the other.

 

Cleaning it up with a grinder is highly unlikely to take it anywhere near a  temperature where annealing would occur, even if you controlled the cooling phase. Clean up one end for use, mount it with that end up and use if for a while. If that end gets bashed up beyond use, clean it up again or flip it over and clean up the other end.