Yes - I've done this twice, successfully using two separate software tools. The key was to use software tools that have image registration and alignment capabilities. There are quite a few available.
The first tool I used, and probably the most flexible, was done using a Panoramic stitching tool, PTAssembler (http://www.tawbaware.com/ptasmblr.htm). Specifically, I set PTAssembler to create a multi layer Photoshop object as it's output. One of PTAssembler's plug-ins automatically aligned the images. To make it work well, shoot your subject with a narrow DOF so that PTAssembler selects only points on the subject to use for image registration and alignment. Otherwise you'll have to manually edit some of the automatically selected 'control points' used to register the image. You'll need to use the PTAssembler setting that accommodates for a moving camera location - called 'Camera Position Optimization'(CPO). You'll need to use CPO, since, relatively speaking, your camera can be considered to be moving in respect to the subject.
There are other Pano tools that may work. For example, you may be able to do this with Hugin, a popular open source Pano tool, but I haven't tried it.
The second software tool I used was one that was developed for 'super-resolution' - PhotoAcute. (http://www.photoacute.com) In this case, I used the older version (version 2.94) that allowed me to save intermediate aligned images. I then stacked those aligned images in Photoshop. This method allowed for more refined 'morphing' of the images to get all of them aligned.
On a side note, depending upon how many images you need to align, what OS restrictions you have, how quickly you can learn new software tools, your budget for the tools, and so forth, you may be better served by manually aligning them in Photoshop. From a level-of-effort perspective, I'd say, if you only have 3 to 4 hours worth of manually alignment, it may not be worth learning new software tools. If you have 20 plus hours of manual alignment, it is definitely worth the investment to learn one of the new tools.
Let us know your decision and please share your results.