Reverse engineering a device can be assisted by tracing lines that are exposed on the PCB. For complex tracing I have used depcb and for more simple tracing I use gimp. First the images of the PCB layers should be aligned with each other.
Recent versions of Gimp allow for preview+opacity during use of "Perspective Tool". On linux this makes manual alignment much easier than the old grid alignment method. To align layers make the master layer visible and set the layer you intend to adjust to invisible. With the adjust layer still selected click on the Perspective Tool. In the tools options and set the opacity for the Image Preview to 50%.
Fotoxx can be used to automatically align and combine two layers. There are 4 options for combining and the following are the results of each for 3 different test cases: top layer skewed, top layer rotated, top layer offset.
Offset
Sample top and bottom) layers offset by a few pixels.
Rotated
Sample top layer rotated a few degrees from bottom) layer.
Skew
Sample top layer is skewed and transformed from bottom) layer.