Hello ; Thank you for writing to us in this forum. fiducial are normally located at the corner of the paste layer, so if you design the fiducials that you are willing to have them half etched you can design them in the solder paste layer and the select the "Etched Half into board" option  You can also leave a note in the stencil remark section and our engineer will notice it as well  further more than all this, you can select the "Confirm Production file" option and this way your order will not enter the production cycle before our system check the necessary requirements that have to match JLC capabilities  About the (top or bottom) selection, it depends on the solder paste that you will use to draw the fiducials, if you want them to be half etched at the top then draw them at the top solder paste layer, if you want them at the bottom side of the stencil then draw them at the bottom solder paste layer of you PCB design. About the half etching of a region, this is possible as long as you put the region at the corner of your PCB design because it will be complicate to define a region for half etching if the region is in the middle of the design. About how to define the side of the etched region, it is similar to the fiducials, use the solder paste layer to draw it. Do not hesitate to ask us if you need any further assistance.

Thank you very much for the detailed answer. That makes things clearer for me.