You need a "V" and an "indent" to keep the sight base from moving while you punch out the pins, and a recess for the pin to drop into. You should be able to see a workable outline laying the base on the 2x4 where you need to remove material.
My method would not be approved by too many here. I took two pieces of very soft white pine inner wall stud, and an old base, sandwiched the old base btw the two pieces of stud, and vise crushed it into the stud pieces.
Did a little drill press clean up, crushed it again, drilled the pin drop holes, and have my own personal tool. And, it works for me. Others mileage ..... variance, and all that.
Best to you. VR