Need of having prefab in Scene

Basically what I have is a prefab-model with all the textures applied etc. ready in Unity to work with.

I also have the script done to Instantiate the prefab to the position I want it to.
But my problem is, that the “original” prefab that I created in unity and added into the script with the Inspector has to remain in the scene?

If I change the visibility or anything of the prefab, the “cloned” one by the script will disappear too. How can I remove the prefab that I only want to create via script from my scene?

Put your prefab in your scene, do anything you want then click apply to apply modification to the original.
Then, in your script put the prefab character and not the scene character in your variable.
Finally delete scene character.