We designed a fairly simple software called PROCAM to do exactly that! It takes 2 Gerber layers - Paste/Mask layer and the Silk layer. Within minutes you can extract all the centroids. PROCAM has a standard excel output with all the centroids, fiducial location and size, step and repeat etc. It can also perform CAD and BOM matching if BOM is available. We have also built Yamaha/Philips VIOS output format, Ipulse .csv format and GenCAD .cad and .pnl output.
We designed this software for one of our very good customer and are now selling it to others as well. It is a very low priced tool.
If you need more information, please write to me at firstname.lastname@example.org.