My newphew is 4 years old I have had him in my care for almost a year now I can't get him inrolled in school or his doctor visits because I don't have custody what do I do his mother passed away and my brother his father is in prison what do I do I need help

You need to get an attorney to file for custody.

This link has some information on how to try to do it yourself, but it may not be possible in all states.
Personally I would rather use a lawyer especially if you would like to try to adopt your nephew; you don't say how long the father is supposed to be in prison, so maybe adoption is the better way to go. Good luck; that child needs you from the sound of it.

http://www.ehow.com/how_8043_file-child-custody.html

I can't tell you how much I admire people like you who
Are willing to take on the monumental task of raising
A child voluntarily .

An attorney is essential.
These matters can be complicated.
With the well being of a child you love involved
It is critical to have a good attorney involved in any dealings with court, child protective services, adoption agencies and any other agencies that may be involved.

God will bless you for this.