This usually depends on the type of node. For example, on a Node2D you will want to save your position. Loading and saving is a complicated process to do, especially when you have many instances.
First you will need to store the data in variables, in case the position would look like this:
var pos = [Vector2(getTheInstancePosition.x,getTheInstancePosition.y)]
I made an array so you can save multiple positions (as you will want to do for so many instances). Once saved you will want to export them from your game and for this you can create a text file. See the link below: