Item Model File Converting

Basically , Like MC's Item pack where the items get converted into item models , how do I do that? So far I only know how to add the particle emitters of the item.

Is there any tools for it or how do I do it?

You don't just "convert" icons into models.

You make geometry based on the icon, maybe map it to use the icon as a texture if you're feeling lucky...

http://www.oinkerwinkle.com is always the first port of call, but for awkwardness like you're suggesting some real modelling software might be a wise investment.

How do I make geometry based on the icon?

Maybe map it to use the icon as a texture? How?

Which program do I use? There is alot of program over at oinkerwinkle's website.

What you want is to learn how to make 3D models. Use all the tools, follow all the tutorials, and that might just get you started on the right track.