How can i set a prefab to x=0 and y=0.

You just need change position of prefab in prefab inspector to 0 0 0 if i understood what you sayed (im not good in english)

I assume you are talking about Instantiating a prefab at run time.

The Instantiate method allows you to set an objects position and rotation when it is created.

 Instantiate(prefab, Vector3.zero, Quaternion.identity);

see docs for more https://docs.unity3d.com/ScriptReference/Object.Instantiate.html

EDIT: Someone mentioned i should explain it a bit better

I made objects, positioned them (without looking at x or y positioning, just dragged them and it looked good). These objects I had to put into another object (a parent) to create my prefab.

Now comes te problem, my parent is positioned at 0.04 for this prefab, but I made more and other parents are positioned between 0-2.

Now when I load in on the screen at 0,0 it is misplaced . Is there any way to place all those objects together down on the y axis instead of all apart.