I was making a Proofgrade Medium Cherry Ply box for someone and was tired of doing a second box as a slip-over cover. I decided to try a flat top with embedded magnets instead. It does work and the magnetic click is satisfying!
Here you can see the underside of the lid with a 3 mm x 1 mm magnet glued in flush. This magnet pocket was cut as a 3.3 mm circle, speed 800, LPI 270, full Pro power. I then used a small file to scratch excess char out of the hole, and secured the magnet with wood glue. (Titebond II and Gorilla Wood Glue both grip those slippery little magnets just fine.)
The tricky part was etching out a matching pocket on the corners of the box body. I had to do test scores on masking tape to get the aim right. With a 3 mm wide magnet there is no margin of error. This project worked, but I probably won’t do this again unless I am using thicker wood, which would make it much easier to get things acceptably lined up.