I use a vacuum chuck to hold my circuit boards flat. With the vacuum system I can maintain .03mm very repeatably.
Check out my website www.drewtronics.net to see the vacuum system.
I have seen that other folks are able to get good results with super glue, and acetone to release the board. Superglue the pcb to a flat piece of aluminum, then cut your traces. Use the acetone to remove the pcb from the aluminum plate.
Another option is carpet tape. 2 sided tape the board to the table, and cut away. Without anything to prevent the board from moving around it can shift under cutting forces, but with a few board stops setup this could be a fine way to cut.
hope that helps