Depends on the parts and the rust. Any rust where gaskets have to sit will have to be cleaned carefully and the surfaces checked properly or the gasket won't seal right. If you have light rust you can sand with wet/dry sandpaper. If the rust is pretty thick you can use a wire brush. There is a gel you can buy in most auto stores near the body repair section. It's a gel that converts rust into a primer-like substance. Worked pretty well for me.
i got my new engine from the junk yard wich the block and heads have rust which i need to get off before i can paint.
I don't want to buy new head gaskets from pulling the heads. if i can paint/squirt some stuff on there that sounds perfect.
Damn! That's a good idea. I don't remember the name of the gel, I'll have to see if I have some still at home. There are also rattle can sprays that will also convert the rust into a primer-like coating. You'll still need to use a wire brush to get off all the loose rust.