How do I choose what size end mill to use?

Depending on what type of work you are doing, different sized end mills could be appropriate.

In terms of length, it is best practice to employ the shortest end mill that gets the job done to decrease chatter, expense, and the risk of breakage. Make sure that the flutes extend farther than the maximum depth that you are cutting.

In terms of diameter, a small radius would be good for more detailed work or tasks like creating square holes, where you wish to avoid large radii in the corners. Larger end mills are advantageous for cutting more material quickly and making deep cuts with lower risk of causing deflection or breakage of the end mill. For more information, see here.