This will explain how to align two layers that are displaced in the X and/or Y direction. This is most often the case with drill layers, which sometimes have a different origin, but can happen with circuit layers also, if exported at different times with different origins.
All the operations to align and move layers are grouped in the submenu shown below:
We will use the "Move Layer Tool" (shortcut Ctrl+Shift+Q). This is a manual operation. The menu above also contains automatic operations that work on groups of layers.
First make visible only the two layers that you are interested in. It is easier to work with the data if the other layers are not visible.
Then activate the "Move Layer Tool". You will be prompted to "Pick and element from the layer to move". Choose an element that has an equivalent in the other layer also. This is usually a pad. Picking pads near the corners of the layers makes the operation easier.
Go near the pad on the layer you want to move and click on it (the green layer in the image below). You are then prompted to "Pick corresponding element on other layer". Now move the cursor close to the corresponding pad on the the other layer (the red layer in the image below) and click on it.
At this point the green layer will be moved so that the two pads picked coincide and you get the desired result (the two layers are aligned):
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