In PCB's I don't think people use photolithography as much as in microchip Fab, instead they use physical stencils, screen-printing or similar patterned sheets placed on top, or direct ink-jet writing (like a printer - slower but ok for a few boards only).
Through-holes in the PCB are often used for alignment. One common way to do this is to place pins through the through-holes, which match up to through-holes in your stencil or other layers, so all layers slot onto the alignment pins prior to applying the paste to the screen.
These holes can be used for front-to-back alignment.
Here are some examples:
However if you actually need to perform photolithography on the PCB, you might be limited by the field-of-view of the Litho tool's microscope. For example, if the litho tool aligns with a microscope that can only view a 0.5mm area, then you need your alignment hole/mark to be smaller than 0.5mm for easy alignment.
A common way around this problem is to make a new "zero layer" just for alignment, and do this first. For example:
- Do photolith or a stencil layer first, defining alignment marks compatible with the Photolith tool (eg. 0.5mm crosses
+), AND define patterns showing where the holes should be drilled for vias •. Also add any other specialized marks as needed. All future layers will thus be registered against this layer.
- Your CNC or manual drill can then align to the Via patterns, while your photolith can align to the crosses etc.
