Align same object in different layers while maintaining integrity of the image

[Annie3500820981t7]

I have multiple photos of the same object, I would like to align all the layers so that the objects lie perfectly on top of one another. Auto-arrange does not work for my purpose as it rarely focuses on the object I want and slightly distorts the image (twisting) and I need to retain the integrety of the scale. I have been doing this using overlay and manually arranging them but I need to do hundreds of sets of photos. Is there a way to set a few reference points on each photo and snap the points together? I am open to any easier way to do achieve this. (I am brand new to photshop)

[Myra Ferguson]

You can select layers and either align their vertical and/or horizontal centers to a selection or the canvas in the Options bar (Window > Options) or by going to Layer > Align > Vertical Centers and Layer > Align > Horizontal Centers.

[Semaphoric]

Several panorama stitching programs allow you to align using control points when the images are side by side, but I don't know if it would work with images on top of each other.

Perhaps one of those photo morphing  softwares, like from the 1990s, could be used.

[Lumigraphics]

Post some examples because I'm struggling to understand the problem.

[LightningPlugins]

If I am understanding what you are trying to do, try this.
-Select all the layers
-choose Edit/Auto_align Layers
-choose Reposition

-OK